Question: mpileup error: reference sequence is not being fetched correctly?
0
gravatar for mkim3
2.1 years 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 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by mkim310
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k 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 2.1 years ago by Jennifer Hillman Jackson25k
1

Thank you Jen for the help!

ADD REPLYlink written 2.1 years ago by mkim310
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