Results of filter_low_expr_transcripts.pl

Question

[arefshamiry]

Dear Sirs,

I used the following trinity script:

...../trinityrnaseq-Trinity-v2.4.0/util/filter_low_expr_transcripts.pl --matrix Trinity_trans.TPM.not_cross_norm --transcripts Trinity.fasta --trinity_mode --min_expr_any 1 --highest_iso_only

and I got results in the terminal window like so:

TRINITY_DN6497_c0_g1_i1 len=446 path=[1:0-445] [-1, 1, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 GTCAAGTCTGTCACTGTCAAGGCTCCTGAATCTGCGACGCACTAGGTGGACAGGTAACTG ATTCCTCATGCCAGTATGCTGGGGGGTTGACTCCGACATAGTGCTTCTGGCGTGGCTTTG GGCCCTTTGCTTGCTCGTGATTTGCACGTGCCTGTTCAGTGGGTTTGATCTATAACATGT GGTGCACTAAGCCATCCTACGATCTTCATCTTCTTCCTCTCTCTTGCTTTCTCTCACAAG CACATCTCTCTCACAATTTTGTTTGCCCTATCTCCCACGCCACCACCACTAGAACAACTA CCATAGGAAGAAGATGAAGTCCATGAAACTTCTGAATATTATGAAAGATTTTAAAAAGTG GGGATAAGTCACAGTCATGTAACTCAATTGATGAGCGCATAAGAACATGCGTGTGTAGAT ACAGTGTTCGATTCTTAGTTATACTA -excluding TRINITY_DN6497_c0_g2_i1, max_expr: 0.9 < 1 -excluding TRINITY_DN6498_c0_g1_i1, max_expr: 0.45 < 1 -excluding TRINITY_DN6499_c0_g1_i1, max_expr: 0.65 < 1

Retained 40364 / 162524 = 24.84% of total transcripts.

But I did not find a file containing these results. My question is how to get all results in a text file?

Thanks a lot and best regards.

Answer 1

[ibasan]

Hi arefshamiry, i think you have to specifiy the output file with > outputfilename.txt:

/trinityrnaseq-Trinity-v2.4.0/util/filter_low_expr_transcripts.pl --matrix Trinity_trans.TPM.not_cross_norm --transcripts Trinity.fasta --trinity_mode --min_expr_any 1 --highest_iso_only > outputfilename.txt

Best