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Question: Bowtie mapping has a unmapped gap on chromosome 6
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gravatar for fang24
21 months ago by
fang24 • 10
fang24 • 10 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 • 604 views
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modified 21 months ago • written 21 months ago by fang24 • 10
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for fang24
21 months ago by
fang24 • 10
fang24 • 10 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 COMMENT • link written 21 months ago by fang24 • 10
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