min_contig_length parameter in Trinity - Isoforms discrimination

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4.2 years ago

Raito92 ▴ 90

Good morning to everyone, I'm trying to build a reference transcriptome from different plant tissues (root, leaf, bud, flower etc), with paired-end Illumina TruSeq reads.

I was wondering... how about the Trinity parameter min_contig_length?

I set a 300 but I've read online it really depends on the single case and whether I woud like to see different isoforms or not in a following phase...

And I'd really like to be able to discriminate among them since I'm analyzing different tissues...

Any suggestions here? Thanks in advance!

transcriptome assembly trinity • 1.0k views

ADD COMMENT • link 4.2 years ago by Raito92 ▴ 90

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you could run trinity without any min length and do filtering afterwards if you want.

the reason of that option is mainly to reduce the amount of noise you get returned by trinity (so be prepared to substantial noise in your result file when running without a min length)

ADD REPLY • link 4.2 years ago by lieven.sterck 15k

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I see, thanks! But I was wondering since I saw different choices in scientific papers what it affects apart from noise?

ADD REPLY • link 4.2 years ago by Raito92 ▴ 90

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