How to "filter_low_expr_transcripts"?
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5.0 years ago
tcf.hcdg ▴ 70

Hello I denovo assembled my samples and then transcript abundance estimatin with RSEM. Now, I would like to filter low expressed transcripts. Fot this I am feeding TPM matrix expression file as well as the Trinity.fasta file to "filter_low_expr_transcripts.pl". I use the following command as mentioned in the mannual:

tb44227@lido-gw02:~/nobackup/Radula_data/trinity_a2b2_seq_111016_1333/RSEM/RSEM_BWT2>~/nobackup/bioinfo_package/trinityrnaseq-2.2.0/util/filter_low_expr_transcripts.pl  --matrix trans_counts.TPM.not_cross_norm --transcripts Trinity.fasta --min_expr_any 5 --highest_iso_only --trinity_mode

and I got the following error message

Error, --min_pct_iso and --highest_iso_only are mutually exclusive parameters.  at /home/tb44227/nobackup/bioinfo_package/trinityrnaseq-2.2.0/util/filter_low_expr_transcripts.pl line 90.

I tried to google it filter_loq_expression_reads but could not find the way to fix it.

Any suggestion to fix this issue:

Thanks

filter TRANSCRIPTS LOW EXPRESSION RNA-Seq • 2.2k views
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Entering edit mode

As the error states, the two parameters are mutually exclusive. You can set the threshold for min_pct_iso for all isoforms, or take the highest one only.

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Thanks. I changed it and It works

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