counting numbers of expressed transcripts

[bprabin]

I ran the kallisto by following the manual provided an got all 3 output files. After that i used the abundance.txt file to count the number of expressed transcripts by using the following script..
/data/trinityrnaseq-2.1.1/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl /data/Prabin_trinity/abundance.tsv
Then I got output for gene counts as a function of minimum TPM value as follow in table
neg_min_tpm num_features
-177001 1
-167389 2

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-201 478288

I got neg_min_tpm value upto -201 ,but should be upto 0 to make a further analysis of expressed genes. Can anyone help me the solve this issue... please...

[pimentel]

@bprabin so sorry for the delayed response. could you send me your output directory in an email?

Thanks!