Question: mpileup error: reference sequence is not being fetched correctly?
0
gravatar for mkim3
19 months ago by
mkim310
mkim310 wrote:

Hi, I ran mpileup using Arabidopsis reference sequence but got an error message in the log file which is below.

[mpileup] 1 samples in 1 input files

<mpileup> Set max per-file depth to 8000

[fai_fetch_seq] The sequence "Pt" not found

[fai_fetch_seq] The sequence "Mt" not found

[fai_fetch_seq] The sequence "4" not found

[fai_fetch_seq] The sequence "2" not found

[fai_fetch_seq] The sequence "3" not found

[fai_fetch_seq] The sequence "5" not found

[fai_fetch_seq] The sequence "1" not found

I have all Ns in reference sequence column when I look at the output file. Can you tell me what I am doing wrong?

Thanks, Minsoo

ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson24k • written 19 months ago by mkim310
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

This looks like a reference genome mismatch problem. There are three Arabidopsis builds at http://usegalaxy.org. If working somewhere else, there could be none or the same or others.

To resolve the problem, make sure that genome/build you select on the MACS2 form is an exact match for the reference genome for the prior mapping steps used to generate the BAM(s).

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson24k
1

Thank you Jen for the help!

ADD REPLYlink written 19 months ago by mkim310
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