Hi Does anyone know how to calculate how much of a genome was covered by an alignment irrespective of the depth at each base? Cheers David
Hi On a separate issue, I have been having trouble generating a corrected fasta file based on a pileup. I have a dataset that is a resequenced genome and I want to correct the fasta file based on the consensus and then re run the alignments to see how it affects things. However, I cannot for the life of me figure out how to do it in Galaxy. Any help appreciated! David
Hello David, Generating a consensus fasta sequence from a BAM or Pile-up file is not yet possible in Galaxy. To date, the Tool Shed also does not have a wrapped/novel tool for this function either. If you or another user were to create such a wrapped tool, it would be most welcome. As would a tool that would replace the corresponding region of the reference genome with the variant fasta sequence to create a novel reference for alignments. Both great ideas that have been discussed a few times on the list and here among our team. If you wanted to open a bitbucket ticket, that would be one way to share exactly what you had in mind and give you a ticket to watch for if/when tools like this are added. Or, I can open one (or possibly two, one for each function) for you, just let me know. https://bitbucket.org/galaxy/galaxy-central/issues?status=new&status=open Thanks for the great feedback, sorry there wasn't a solution (yet!), Best, Jen Galaxy team On 7/22/11 12:56 PM, David Matthews wrote:
Hi
On a separate issue, I have been having trouble generating a corrected fasta file based on a pileup. I have a dataset that is a resequenced genome and I want to correct the fasta file based on the consensus and then re run the alignments to see how it affects things. However, I cannot for the life of me figure out how to do it in Galaxy. Any help appreciated!
David
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Jen/ Jeremy/ Galaxy team, Is there any plan of implementing gene fusion version of TopHat in Galaxy perhaps in next few months or so? Alternatively, if some one has used with gene fusion using TopHat in Galaxy frame work please share. Thanks. Vasu Punj
Hi people, I have a litle problem with Bowtie alignments. I am tryin to align sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps (detailed below) I only obtain reads of 15-18nt, and I know that I have a lot of microRNAs (20-22nt) in my data. Beside the size problem, I realized that when the reads and the reference (the precursor in any case) the sequences don't match as I would expect. The sequential steps that I've made: - Groom - Clip (adaptor elimination) - Bowtie against hairpin database (mirBase precursor) - SAM-to-BAM - Download Bam and Bai files - Open in IGV the file and the hairpin database May be I am doing something really bad, but I dont know. Any help/suggestion/tip? Thanks in advance
Hello Christian, I found this FAQ on the IGV web site. They may be the best resource for resolving display issues if they continue. Comparing results between IGV and Galaxy's visualization tool Trackster can help you to determine the root cause of the problem. http://www.broadinstitute.org/software/igv/BAM http://www.broadinstitute.org/igv/FAQ Hopefully this helps point you in the right direction, Best, Jen Galaxy team On 7/31/11 6:04 PM, Cristian Rojas wrote:
Hi people, I have a litle problem with Bowtie alignments. I am tryin to align sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps (detailed below) I only obtain reads of 15-18nt, and I know that I have a lot of microRNAs (20-22nt) in my data. Beside the size problem, I realized that when the reads and the reference (the precursor in any case) the sequences don't match as I would expect. The sequential steps that I've made: - Groom - Clip (adaptor elimination) - Bowtie against hairpin database (mirBase precursor) - SAM-to-BAM - Download Bam and Bai files - Open in IGV the file and the hairpin database
May be I am doing something really bad, but I dont know. Any help/suggestion/tip? Thanks in advance
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Hi Vasu, The Galaxy team doesn't have any plans to add this tool in the near future. Best, J. On Jul 30, 2011, at 1:35 AM, vasu punj wrote:
Jen/ Jeremy/ Galaxy team,
Is there any plan of implementing gene fusion version of TopHat in Galaxy perhaps in next few months or so? Alternatively, if some one has used with gene fusion using TopHat in Galaxy frame work please share.
Thanks.
Vasu Punj ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I have some code which can do most of the requested things. Let me figure out how to galaxy around it, and I'll submit it. John Sent from my mobile device On 2011-07-30, at 12:47 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello David,
Generating a consensus fasta sequence from a BAM or Pile-up file is not yet possible in Galaxy. To date, the Tool Shed also does not have a wrapped/novel tool for this function either.
If you or another user were to create such a wrapped tool, it would be most welcome. As would a tool that would replace the corresponding region of the reference genome with the variant fasta sequence to create a novel reference for alignments.
Both great ideas that have been discussed a few times on the list and here among our team. If you wanted to open a bitbucket ticket, that would be one way to share exactly what you had in mind and give you a ticket to watch for if/when tools like this are added. Or, I can open one (or possibly two, one for each function) for you, just let me know.
https://bitbucket.org/galaxy/galaxy-central/issues?status=new&status=open
Thanks for the great feedback, sorry there wasn't a solution (yet!),
Best,
Jen Galaxy team
On 7/22/11 12:56 PM, David Matthews wrote:
Hi
On a separate issue, I have been having trouble generating a corrected fasta file based on a pileup. I have a dataset that is a resequenced genome and I want to correct the fasta file based on the consensus and then re run the alignments to see how it affects things. However, I cannot for the life of me figure out how to do it in Galaxy. Any help appreciated!
David
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi John, That would be totally fantastic - many thanks! Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk On 30 Jul 2011, at 16:35, John Nash wrote:
I have some code which can do most of the requested things. Let me figure out how to galaxy around it, and I'll submit it.
John
Sent from my mobile device
On 2011-07-30, at 12:47 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello David,
Generating a consensus fasta sequence from a BAM or Pile-up file is not yet possible in Galaxy. To date, the Tool Shed also does not have a wrapped/novel tool for this function either.
If you or another user were to create such a wrapped tool, it would be most welcome. As would a tool that would replace the corresponding region of the reference genome with the variant fasta sequence to create a novel reference for alignments.
Both great ideas that have been discussed a few times on the list and here among our team. If you wanted to open a bitbucket ticket, that would be one way to share exactly what you had in mind and give you a ticket to watch for if/when tools like this are added. Or, I can open one (or possibly two, one for each function) for you, just let me know.
https://bitbucket.org/galaxy/galaxy-central/issues?status=new&status=open
Thanks for the great feedback, sorry there wasn't a solution (yet!),
Best,
Jen Galaxy team
On 7/22/11 12:56 PM, David Matthews wrote:
Hi
On a separate issue, I have been having trouble generating a corrected fasta file based on a pileup. I have a dataset that is a resequenced genome and I want to correct the fasta file based on the consensus and then re run the alignments to see how it affects things. However, I cannot for the life of me figure out how to do it in Galaxy. Any help appreciated!
David
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello David, To calculate coverage, please see the tool "Regional Variation -> Feature coverage". Query and target must both be in Interval/BED format. Query data in Interval/BED format is possible in most of the dataflow paths through the tools and from external sources. The reference genome file will likely need to be imported and formatted. This is simple example history where I pulled the chromInfo file from UCSC and formatted, extracted a subset of genes in BED format, and ran the "Feature Coverage" tool (both directions, see datasets 8 and 9). http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/galaxy-user-calculating-perc... Hopefully this helps, Jen Galaxy team On 7/22/11 12:32 PM, David Matthews wrote:
Hi
Does anyone know how to calculate how much of a genome was covered by an alignment irrespective of the depth at each base?
Cheers David
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
Hi Jen, Many thanks for this, on a related subject do you know of a way to correct a FASTA file on the basis of a pileup (or even just on the BAM file)? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk On 25 Jul 2011, at 17:52, Jennifer Jackson wrote:
Hello David,
To calculate coverage, please see the tool "Regional Variation -> Feature coverage". Query and target must both be in Interval/BED format. Query data in Interval/BED format is possible in most of the dataflow paths through the tools and from external sources. The reference genome file will likely need to be imported and formatted.
This is simple example history where I pulled the chromInfo file from UCSC and formatted, extracted a subset of genes in BED format, and ran the "Feature Coverage" tool (both directions, see datasets 8 and 9).
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/galaxy-user-calculating-perc...
Hopefully this helps,
Jen Galaxy team
On 7/22/11 12:32 PM, David Matthews wrote:
Hi
Does anyone know how to calculate how much of a genome was covered by an alignment irrespective of the depth at each base?
Cheers David
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
participants (6)
-
Cristian Rojas -
David Matthews -
Jennifer Jackson -
Jeremy Goecks -
John Nash -
vasu punj