Question: two samples with 0% alignment
0
gravatar for demoraesdiogo2017
26 days ago by
demoraesdiogo201740 wrote:

I have about 12 samples I aligned with mm39. All samples had good quality reads and all paired, as trimmomatic gave me empty files for unpaired reads. Strangely, two of them had 0% alignment with the genome. I blasted a few reads and they seem to match mus musculus or other rodents. I'm using HISAT2 on galaxy. Is it a bug?

hisat2 rna-seq galaxy • 83 views
ADD COMMENTlink written 26 days ago by demoraesdiogo201740
1
gravatar for GenoMax
26 days ago by
GenoMax96k
United States
GenoMax96k wrote:

If you are using PSU public galaxy then please post this on their help forum for prompt response: https://help.galaxyproject.org/

That said this could just be failed jobs on galaxy so no harm in re-trying the alignments.

ADD COMMENTlink written 26 days ago by GenoMax96k

sure I will delete the post here and post there

ADD REPLYlink written 26 days ago by demoraesdiogo201740

I have undeleted the post so that others can see what the right course of action is if they have similar questions.

ADD REPLYlink written 26 days ago by Istvan Albert ♦♦ 86k
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