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Question: HISAT error msg or 0% alignment.
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gravatar for sa.kim.227
21 months ago by
sa.kim.227 • 10
sa.kim.227 • 10 wrote:

Hi, I'm very new to Galaxy and RNA-seq in general. I can't seem to figure out why we are getting this problem every time I try to run HISAT on one of my fastq file.. I've been using Human genome hg38 as the reference genome but I've also tried the other 5 as well and I either get 0% alignment or this error message. What am I doing wrong?

(ERR): hisat2-align died with signal 11 (SEGV) (core dumped) [E::sam_parse1] SEQ and QUAL are of different length [W::sam_read1] parse error at line 483 [bam_sort_core] truncated file. Continue anyway.
rna-seq hisat • 669 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by sa.kim.227 • 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,

We addressed this through a bug report yesterday, correct? The inputs had a format issue that needed to be corrected.

If that was not your bug report, please send in a bug report from the error dataset and we'll review for more feedback. Include a link to this post in the comments please and leave all datasets undeleted. If you have already sent in a bug report, reply to it with a link to this question, so I can find and assess the problem. https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks, Jen
ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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