Warning meassage in mode 2: Unable to calculate gene expression!

[Lynuxoo]

As mentioned in #19 , I got a warning message when calculating transcripts expression.

Unable to calculate gene expression! Including all transcripts with at least one read to the downstream analysis...

I change the line 49 of the mode2_alignment.py script:

subprocess.call(['express',` '-o', str(f"{aln_dir}/fpkm_counts"), '-O', '1', '--output-align-prob', '--no-bias-correct', str('--' + str(args.strand)), str(args.transcripts), str(f"{aln_dir}/genes.bam")], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)

to

subprocess.call(['express',` '-o', str(f"{aln_dir}/fpkm_counts"), '-O', '1', '--output-align-prob', '--no-bias-correct', str('--' + str(args.strand)), str(args.transcripts), str(f"{aln_dir}/genes.bam")])

And then it prints:

[Tuesday 19/3/2024 - 18h:27]    Calculating transcripts expression...
2024-Mar-19 18:27:21 - Command-Line Argument Error: unknown option fwd-stranded.
2024-Mar-19 18:27:21 - Command-Line Argument Error: target sequence fasta file required.
express v1.5.1
-----------------------------
File Usage:  express [options] <target_seqs.fa> <hits.(sam/bam)>
Piped Usage: bowtie [options] -S <index> <reads.fq> | express [options] <target_seqs.fa>

Required arguments:
 <target_seqs.fa>     target sequence file in fasta format
 <hits.(sam/bam)>     read alignment file in SAM or BAM format

It seems that there is something wrong with bowtie. Did I enter the wrong parameters?

Thanks for your explanation!

[Lynuxoo]

Hello,

Additionally, I've noticed that in the chimreads_evidence_FINAL.tsv results file from ChimeraTE analysis, all values in the "transcript_FPKM" column are "NA". Could this be related to the earlier warning?

Appreciate any insights.