repeatmask fasta file

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5.5 years ago

lkianmehr ▴ 100

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?

repeatmask TEelements Salmon Index • 1.5k views

ADD COMMENT • link updated 5.4 years ago by Biostar 20 • written 5.5 years ago by lkianmehr ▴ 100

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

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Please do the same for your previous posts as well.

ADD REPLY • link 5.5 years ago by GenoMax 141k

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

This needs more information.

ADD REPLY • link 5.5 years ago by WouterDeCoster 47k

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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 REPLY • link 5.4 years ago by lkianmehr ▴ 100

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