Is it advised to remove transcripts with zero unique_hits?

[weishwu]

Hi,

I'm using MMSeq to quantify haplotype-specific expression. I wonder if it is advised to filter out the transcripts/genes that:
(1) have zero "unique_hits" in the *.mmseq file
and
(2) have identical haplotype sequences as indicated in *.identical.mmseq file

Thanks,

[eturro]

1) I wouldn't filter out the ones with zero unique_hits. 2) The "identical" transcripts have exactly the same sequence so yes I would use the aggregate summaries in the *identical.mmseq files.

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On 6 Sep 2019, at 14:01, weishwu ***@***.***> wrote: Hi, I'm using MMSeq to quantify haplotype-specific expression. I wonder if it is advised to filter out the transcripts/genes that: (1) have zero "unique_hits" in the *.mmseq file and (2) have identical haplotype sequences as indicated in *.identical.mmseq file Thanks, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[weishwu]

Thanks!