abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
Entering edit mode
4 weeks ago
jway • 0

Hello, I'm using dockerized Trinity (Trinity-v2.15.1) to run the abundance_estimates_to_matrix.pl script. I have already used Kallisto to run the align_and_estimate_abundance.pl script. However, when I run abundance_estimate_to_matrix.pl, I get the following:

(base) jackieway@LabDTGenome2404:~$ docker run -v `pwd`:`pwd` trinityrnaseq/trinityrnaseq /usr/local/bin/util/abundance_estimates_to_matrix.pl --est_method kallisto --gene_trans_map /home/jackieway/trinity_out_dir_sortednew.Trinity.fasta.gene_trans_map /home/jackieway/abundance.tsv
-reading file: /home/jackieway/abundance.tsv

* Outputting combined matrix.

Warning, only one sample, so not performing cross-sample normalization

The Trinity wiki tells me that the following 3 files are supposed to be generated (kallisto.isoform.counts.matrix, kallisto.isoform.TPM.not_cross_norm, kallisto.isoform.TMM.EXPR.matrix), but I cannot find them anywhere in /home/jackieway, or anywhere else. Am I using abundance_estimates_to_matrix.pl correctly? My abundance.tsv file and my gene_trans_map file are too large to be attached, but here are the first 10 lines of each. Any insight would be greatly appreciated.

target_id   length  eff_length  est_counts  tpm
TRINITY_DN400489_c0_g1_i1   300 162.19  3   0.0620998
TRINITY_DN400497_c0_g1_i1   237 105.791 2   0.0634709
TRINITY_DN400569_c0_g1_i1   250 116.997 3   0.0860877
TRINITY_DN400481_c0_g1_i1   201 76.2273 12  0.528523
TRINITY_DN400539_c0_g1_i1   241 109.157 11  0.338326
TRINITY_DN400491_c0_g1_i1   231 100.771 9   0.299847
TRINITY_DN400546_c0_g1_i1   255 121.331 23  0.636427
TRINITY_DN400487_c0_g1_i1   211 84.3347 3   0.119428
TRINITY_DN400556_c0_g1_i1   238 106.62  2   0.0629775

TRINITY_DN400489_c0_g1  TRINITY_DN400489_c0_g1_i1
TRINITY_DN400497_c0_g1  TRINITY_DN400497_c0_g1_i1
TRINITY_DN400569_c0_g1  TRINITY_DN400569_c0_g1_i1
TRINITY_DN400481_c0_g1  TRINITY_DN400481_c0_g1_i1
TRINITY_DN400539_c0_g1  TRINITY_DN400539_c0_g1_i1
TRINITY_DN400491_c0_g1  TRINITY_DN400491_c0_g1_i1
TRINITY_DN400546_c0_g1  TRINITY_DN400546_c0_g1_i1
TRINITY_DN400487_c0_g1  TRINITY_DN400487_c0_g1_i1
TRINITY_DN400556_c0_g1  TRINITY_DN400556_c0_g1_i1
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