Question about aaChange tool.
by Maha Al Kahtani
Hello,
Recently i have used galaxy to find corresponding amino acids to a list of
SNPs that i have. i used aaChange tool from the tool panel for this
purpose. After obtaining the result i checked the correctness of this
results by searching dbSNP for randomly chosen SNPs. however, some of those
SNPs mapped to incorrect amino acid,
For example,
The SNP( rs11549096), was mapped by Galaxy to the change ( Asp:Tyr/His, ) ,
Searching the dbSNP for this SNP Shows that the Change should be Asp :Asn
and the link for this SNP in the dbSNP is :
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_sea...
So, the reference is correct in all cases i searched (more than a
thousand), the position of change in the aa is correct, *but* the
alternative aa is not correct in all cases.
What causes this mistake, and how to solve this problem?
Note: my list contains hundreds of thousands of SNPs, so, i can not check
each one of them.
prompt response is appreciated,
Best Regards,
Maha
10 years, 3 months
Tophat error
by David Matthews
Hi,
JUst running a TopHat job which returned the following error:
Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Mar 13 12:45:08 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942
format: fastq
quality scale: phred33 (default)
[Tue Mar 13 12:45:21 2012] Preparing reads
left reads: min. length=56, count=29523921
right reads: min. length=56, count=29543412
[Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie
[Tue Mar 13 13:45:26 2012] Processing bowtie hits
[Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2)
[Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2)
[Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie
[Tue Mar 13 15:37:46 2012] Processing bowtie hits
[Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2)
[Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2)
[Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
Traceback (most recent call last):
File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3063, in <module>
sys.exit(main())
File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3029, in main
user_supplied_deletions)
File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 2681, in spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers, not str
Does anyone know what this kind of error is?
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(a)bristol.ac.uk
10 years, 3 months
Maq consensus calling changes quality score of the read?
by Antony Jose
Hi,
We used the generate pileup tool with consensus base calling option using
Maq. In the output, the quality scores of the bases were changed. For
example if the input score of bases in the SAM file were 'IIJIH'. They were
changed to '22321'. Is this a glitch or is this expected? Thank you.
Antony
10 years, 3 months
Tophat error
by David Matthews
Hi,
JUst running a TopHat job which returned the following error:
Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Mar 13 12:45:08 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942
format: fastq
quality scale: phred33 (default)
[Tue Mar 13 12:45:21 2012] Preparing reads
left reads: min. length=56, count=29523921
right reads: min. length=56, count=29543412
[Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie
[Tue Mar 13 13:45:26 2012] Processing bowtie hits
[Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2)
[Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2)
[Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie
[Tue Mar 13 15:37:46 2012] Processing bowtie hits
[Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2)
[Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2)
[Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
Traceback (most recent call last):
File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3063, in <module>
sys.exit(main())
File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3029, in main
user_supplied_deletions)
File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 2681, in spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers, not str
Does anyone know what this kind of error is?
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(a)bristol.ac.uk
10 years, 3 months
Question about plotting circos plot
by shamsher jagat
I wonder if is it possible to visualize mutation data in circular plot
termed as circos plot e.g
@http://www.eurekalert.org/multimedia/pub/31019.php?from=181881
Any suggestion for an alternative tool will also be appreciated.
Thanks
Shamsher
10 years, 3 months
Quick question on generated tables
by Carly Hom
Hello,
I am working on a project that involves extracting a list of promoter
regions that contain a significant enough H3k27me3 signal. So far I have
produced an output in the ENCODE genome browser which is great for the
visual representations I will be needed, but I also need to extract the
table that was generated. I see the first few lines in a snapshot of the
data that galaxy provided me with, but how do I extract that entire table
into spreadsheet or txt format? If you could enlighten me on a galaxy
function that allows me to do this and I may be glancing over that would be
great. I have provided an image of the data that I want to extract from
galaxy so there is no confusion of what I am trying to do. Thank you!
- Cary
--
Caroline Hom
Engineering Residential Community Peer Mentor
School of Biological and Health Systems Engineering Grader
Fulton Undergraduate Teaching Assistant
Fulton Undergraduate Researcher, Synthetic Biology and Bioinformatics
Tempe, AZ
Ph: 602-315-5728
Arizona State University | Ira A. Fulton Schools of Engineering
B.S.E. Biomedical Engineering
OpenWetWare <http://openwetware.org/wiki/User:Caroline_Hom>
LinkedIn<http://www.linkedin.com/profile/view?id=139737398&locale=en_US&trk=tab_pro>
10 years, 3 months
Error using intersect tool: "problem: 536870912 is larger than the size of this BitSet (536870912)."
by Tim Reddy
Hello,
I'm getting this problem a lot when I'm trying to intersect data sets.
There errors are similar to:
Skipped 4 invalid lines of 1st dataset, 1st line #19614: "chr10
135498863 135499333 chr10.6783 1000 + 0.4037 15.3 -1 236
", problem: 536870912 is larger than the size of this BitSet (536870912).
This is on the main public server with the hg19 genome while running
"overlapping pieces of intervals" on pairs of datasets in the attached
history. I've tried different format types, changing the strand,
confirming that the provided files to not extend past end of
chromosomes, to no avail.
Public history: http://main.g2.bx.psu.edu/u/timreddy/h/unnamed-history
Seems there was an error to this extent in the archives from 2009, but
no response.
Tx,
Tim
--
Timothy E. Reddy, Ph.D.
Assistant Professor
Department of Biostatistics and Bioinformatics
Institute for Genome Sciences and Policy
Duke University School of Medicine
919-684-3286 (lab)
919-564-9536 (cell)
tim.reddy(a)duke.edu
10 years, 3 months
Dataset name in dataset file
by Cittaro Davide
Hi all,
I have a question about a weird usage of galaxy: suppose I have 23 files, each for a chromosome, suppose the dataset name (in history) contains the chromosome name but the dataset content don't (i.e. I only have chrom position and 2 associated values), is there a way to add a column so that the content of the column contains the dataset name? In a automatic way, I mean...
i.e.
data-chr1
1000000 3.1 23
1000100 1.2 23
[…]
data-chr2
1234411 33.1 24
4225211 12.0 44
[…]
I would like them to be
data-chr1 1000000 3.1 23
data-chr1 1000100 1.2 23
[…]
data-chr2 1234411 33.1 24
data-chr2 4225211 12.0 44
[…]
So that I can merge them and strip 'data-'...
Oh, I know I can do it outside galaxy and upload the final file, but I would like to know if (and how) this is possible,
d
/*
Davide Cittaro, PhD
Head of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy
Office: +39 02 26439140
Mail: cittaro.davide(a)hsr.it
Skype: daweonline
*/
10 years, 3 months
Problem Interset interval tools
by Mónica Pérez Alegre
Hi
I´m this problema when I Try to use Intersect uintervals tools:
Info: Skipped 6 invalid lines of 1st dataset, 1st line #1258: "chr9 357415 360396 ORF - YIR002C MPH1 S000001441 Active Verified 2982
", problem: 536870912 is larger than the size of this BitSet (536870912).
Some idea?
Thanks
regards
☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications
Mónica Pérez Alegre, PhD
Genomics Unit
CABIMER-CSIC
Edif. CABIMER - Avda. Américo Vespucio s/n
Parque Científico y Tecnológico Cartuja 93
41092 Seville-SPAIN
Tlf: +34 954 467 828
Fax: +34 954 461 664
www.cabimer.es<http://www.cabimer.es/>
http://www.cabimer.es/web/es/unidades-apoyo/genomica
10 years, 3 months
Extracting number of reads from Bowtie analysis
by Jerzy Dyczkowski
Hello, I am new here!
I am aligning Solexa files to genome using tool: NGS: Mapping: Map with
Bowtie for Illumina.
My question: What is the most easy way to check the number of aligned
reads in the output from above?
I couldn't find this number directly. I found a way, but it looks
circular and unoptimal: to run Bowtie with option: put umapped reads
into the file, download the file, open it, count reads, subtract from
reads in the original file. However, downloading large files is
time-consuming, and I am sure the easier way is somewhere.
Further question: good link to help on how to improve number of reads
from ChIP study aligned to mouse genome would be also appreciated.
best regards,
Jerzy
10 years, 3 months
