Question: Bowtie mapping has a unmapped gap on chromosome 6
1
gravatar for fang24
9 months ago by
fang2410
fang2410 wrote:

Hi, Recently, I used Galaxy Bowtie to map my ChIP-seq data to human genome, However, I saw a big gap on Chromosome 6 that can not be efficiently mapped.to verify it is not because of my data, I re-mapped another data that was mapped correctly before. The gap appeared in this old data where the old mapping was fine. Does anyone else experiencing the same problem? What should I do about this? Thanks, Ninuo

chip-seq • 276 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by fang2410
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

I suggest double checking that the tool version, all inputs (include reference data), and settings were exactly the same between the original run and the rerun.

If the above checks out, my next troubleshooting guess is that the genome index the tool is accessing has a problem. Where are you using Galaxy? The Main server at http://usegalaxy.org or elsewhere? What exact genome (database) and tool (+ version) are you using?

Let's start there. Once you do the checks and share more details (if needed), we can decide how to proceed. Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson23k
0
gravatar for fang24
9 months ago by
fang2410
fang2410 wrote:

Hi, Jen, Thank you for the swift response! I am using the usegalaxy.org website. using genome hg19 (2009) and Map with Bowtie for Illumina (Galaxy Version 1.1.2) I used default bowtie settings with one exception: Suppress all alignments for a read if more than n reportable alignments exist n=1 Ninuo

ADD COMMENTlink written 9 months ago by fang2410
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