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Re: [galaxy-user] fastqc and blast?
by Jennifer Jackson 14 Dec '13

14 Dec '13

Hello Mark, Correct - no needed. Any Illumina data that results from a CASAVA 1.8 or higher pipeline is already has quality scores scaled to Sanger Phred with an ASCII offset of 33. This translates to the ".fastqsanger" format in Galaxy, so no grooming is required, you can just assign the datatype. How to do that is in the first link below. And all the details, including how to read a FastQC report to determine this is in the screencast. Thanks! Jen Galaxy team On 12/13/13 8:58 AM, Mark Lindsay wrote: > Hi James > > do you need to run the Groomer on the latest Illumina data? > > BW > > Mark > > > > On 13 Dec 2013, at 16:53, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > >> Hello, >> >> For the first question, make sure that you are running the groomer >> with the correction options. In almost all cases for Illumina data >> this will mean leaving all but one setting at default. The setting to >> change is "Input FASTQ quality scores type:". The results of FastQC >> will inform you about how to set this. An example is in this wiki >> section's screencast plus the first bullet point: >> https://wiki.galaxyproject.org/Support#Dataset_special_cases >> http://vimeo.com/galaxyproject/fastqprep >> >> For the second, I am not sure what you mean by 'different'. Do you >> mean the data may have contamination from another species? Or that >> the the data content may be different with respect to quality? >> >> In short, to filter based on quality as reported in the FastQC >> report, try tools in the same tool group such as "FASTQ Trimmer" or >> "FASTQ Quality Trimmer". >> >> The protocols included in our RNA-seq pipeline help start out with >> some quality steps: >> https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq >> >> And many from our community have contributed RNA-seq tutorials: >> https://wiki.galaxyproject.org/Learn#Other_Tutorials >> >> Hopefully this helps! >> >> Jen >> Galaxy team >> >> On 12/13/13 7:05 AM, Jorge Braun wrote: >>> Hello mates, >>> >>> I have two doubts galaxy: >>> >>> a) I have rna-seq data from Illumina and do fastqc ... the results >>> are good but when I fastgroomer to Sanger format and then fastqc ... >>> the results are bad. Does anyone know the cause? I do not understand >>> why. >>> >>> b) With the same sequences can know if they are different Rna and >>> eliminate those that do not want to examine? >>> >>> merry christmas :) >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> atusegalaxy.org <http://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: >>> >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org <http://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: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Which tool to use for extract exon, codon information
by Tomaszewicz, Keith 12 Dec '13

12 Dec '13

Hi, I am new to galaxy but I think your tools may be what I need. I simply have a .bed file with amplicons and their chromosome, start and stop location in the human genome. I simply want to align the .bed file amplicons to the HG19 and have a file I can export that which will tell me what exons are covered by the amplicons. Is this possible? If so I have no idea how to do this yet using galaxy. Do I need to upload the HG19 or is that in your system already. Can codons that are covered by the start and stop locations be extracted as well.? Thanks keith ...................................................................... The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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inconsistent BAM-to-SAM behavior
by Michael Mason 11 Dec '13

11 Dec '13

Hi, I have run some top hap output through the samtools BAM-to-SAM wrapper. It creates the SAM file about 50% of the time. The rest of the time it makes an empty file. In this case if I just rerun it often works. I was wondering if anyone else has seen this behavior. I am using a cloud server and think I might need to change some settings. This causes my workflow to fail for many libraries so I also interested in any workarounds anyone has figured out. Thanks in advance for any help. Cheers Mike ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Workflow does not run
by garzetti 11 Dec '13

11 Dec '13

Hello! I have a question about a workflow I have created from my history. I can edit and view it, but when I try to run it, a white page appears and I cannot do anything. I have created other worflows which perfectly run, but I don't know why this one doesn't. It includes 4 steps for GATK pre-processing steps (Indel Realigner, Count Covariates and Table Recalibration). What can the problem be? I would appreciate any input! Thanks Debora

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My Galaxy runs are still not starting
by Afazja - mpm 10 Dec '13

10 Dec '13

Hi I have seen a similar posts on Galaxy mailing list and writing to you since my problems with Galaxy continues. I have jobs (Cofflinks and Tophat) which have been waiting to run for a more then 12 hours. Is there a problem with jobs running on Galaxy today? Many hanks Marcin

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How to filter the sequences containing not[ATCG] character？
by 朱师云 10 Dec '13

10 Dec '13

Hi Jen,As the title, I have a [fasta] file that obtained from a [gtf] file, >cuff102.1atcgtaaagggcgat>cuff103.1gtcgttgactNNNNNNNNgtc and I want to get the output like this to filter the sequences that contain any not[ATCG] character? >cuff102.1atcgtaaagggcgat I have a large of sequences to filter. I thought a way that firstly convert the file to [interval] file, and secondly SELECT the line not matching the patten /\t[ATCGatcg]*[^ATCGatcg]/.Am I right? Or there is a one-step way ?

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Empty bowtie2 output
by IIHG Galaxy Administrator 10 Dec '13

10 Dec '13

In follow-up to http://user.list.galaxyproject.org/Empty-bowtie2-output-tp4656137.html, is there: - an ETA on when the issue with Bowtie2, in August 2013 distribution, generating empty output will be fixed (if not already fixed) ? - a suggested workaround (revert to an older version of that particular tool etc.) in the meantime ? Thank you. Unrelated: wasn't able to determine how to update that thread to request status, hence creating a new one.

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Problem with executable file in FastQC
by Jorge Braun 09 Dec '13

09 Dec '13

Hi mates!! I have a problem with Galaxy... FastQC doesn't run because the file FastQC.py cann't find executable file FastQC.xml. Almost, that file is in the same directory called rgenetics, (seeing Linux terminal) . someone can help me? thanks and have a nice day :)

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Trackster Error chrom/?.len , No such file or directory
by Jasper Jan Koehorst 06 Dec '13

06 Dec '13

I have my own genome fasta file containing 1 chromosome with a modified header so that it looks like: >chr1 ATGCATGC.... I did a FASTQ mapping on it via the galaxy interface and now I end up with a bam file: 9 Bowtie2 on data 6, data 8, and data 7: aligned reads 1.2 GB format bam database ? I use the visualize button to start the visualization of the dataset. I chose trackster, And view it in a new visualization. I use my fasta file as a reference genome: NameKeyNumber of chroms/contigsSTPmg315STPmg315_v11 But then I get the error: Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len , No such file or directory I looked into the /chrom/ folder and of course ? does not exist. I am currently running python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ But this ofcourse downloads only known genomes and their chr. information. As I have my own genome I was curious how to continue with this. I manually created a file in the /chrom/so that it looks like this: *head STPmg315.len * chr1 1900521 but no luck so far. What else do I have to do to make it work? Thanks, Jasper

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.Bam file upload and use problem
by Lu, Yuan (MU-Student) 05 Dec '13

05 Dec '13

Recently I was trying to use Galaxy for my data analysis but ran into problems..... Condition: I used galaxy server at PSU. I tried load local .bam file directly to galaxy, I also tried FTP, but both ways resulted into the same outcome. The .bam files I was using are pure .bam files with no index. Problems: 1.After I load them, the file was recognized as .txt file, and it is "empty" (But it did take long time to upload to FTP ~1GB), in the annotation window, it shows "The uploaded binary file contains inappropriate content" 2. I tried to convert the file to .bam format, it returns "An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection." Anyone know how to solve this problem? Y.L.

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