Question: repeatmask fasta file
0
gravatar for lkianmehr
11 months ago by
lkianmehr30
France
lkianmehr30 wrote:

Excuse me, I am confused about choosing repeatmask fasta file from repbase, actually, I used Mouse.RepeatMasker.masked.fa from repbase to make an index by Salmon but output was incomplete, and Salmon is not able to make quantification on it, why? is the input file correct or I should choose another one?

ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 11 months ago by lkianmehr30

lkianmehr : Don't forget to follow up on your past threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

Please do the same for your previous posts as well.

ADD REPLYlink written 11 months ago by genomax72k

output was incomplete, and Salmon is not able to make quantification on it, why?

This needs more information.

ADD REPLYlink written 11 months ago by WouterDeCoster41k

sorry for the delay, I checked repeat-mask index by Salmon, only there are 5 files, I think making index is not completely done, don't know why! just set k-mer 3 and receive this warning:

[jointLog] [warning] Entry with header [chr1] was long er than 200000 nucleotides. Are you certain that we are indexing a transcriptom e and not a genome? what should I do now?

ADD REPLYlink modified 11 months ago • written 11 months ago by lkianmehr30
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