I just installed a new instance of Galaxy and bwa_wrappers from the main
toolshed. I then uploaded a reference genome along with two FASTQ files in
order to run "Map with BWA for Illumina". When I run it, I get this error:
The alignment failed.
Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwt_restore_bwt] fail to open file
I've used the same tool on other Galaxy instances and it always
auto-indexes the reference genome here before continuing. What's going
wrong? (I made sure bwa was in the user's PATH that is running run.sh)
Is it possible to upload files from the NCBI sra data base, then use fastq-dump from the sra toolit within galaxy? If not, could these tools be added?
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I wonder if Galaxy take SOLiD XSQ format data as input for mapping. I know it takes csfasta/qual data.
Does anyone try this kind of analysis with SOLiD XSQ format?
Any feedback and advice is appreciate it.
Earlier today I couldn't add a new visualization. I just was working again
and now I cannot load the viualizations that I'd previously set to load (BAM
from SAV). I get the message
Internal Server Error
Galaxy was unable to sucessfully complete your request....
GURU MEDITATION: #ff39a25b2b684850ba01c9bdc9eb8942
Thanks for your help!
de Jong Laboratory
In my account I have uploaded a file name iso_mm10.bed. The bed files
contains coordinates of 6018 isochores of mouse genome mm10. I want to
extract GC% of each scores with the list of genes present in each isochores.
I tried using extract features, geecee, and many other tools from galaxy.
But every time either it said error or no peak.
I will be grateful to you if you kindly give me an idea about how to solve
Abdullah Al Mahmud, PhD
University of Montreal,
Lab. of Dr. Jacques Michaud
CHU Sainte-Justine Research Center,
Montreal, Quebec, Canada.