Description of the bug
Hello,
first of all thanks for providing the pipeline! I've been testing the STAR Salmon branch and I've realised that when starting the pipeline with fastq files, Salmon takes the unsorted *.Aligned.toTranscriptome.out.bam files as input, which is correct, but when starting the pipeline from these transcriptome BAMs, it first sorts them with Samtools and then it takes the sorted files as input, which is not correct, as indicated by Salmon developers:
" One of the fundamental assumptions of such inference methods is that observations (i.e. reads or alignments) are made “at random”. This means, for example, that alignments should not be sorted by target or position."(https://salmon.readthedocs.io/en/latest/salmon.html).
Thanks and best,
Alba
Command used and terminal output
Relevant files
No response
System information
No response
Description of the bug
Hello,
first of all thanks for providing the pipeline! I've been testing the STAR Salmon branch and I've realised that when starting the pipeline with fastq files, Salmon takes the unsorted *.Aligned.toTranscriptome.out.bam files as input, which is correct, but when starting the pipeline from these transcriptome BAMs, it first sorts them with Samtools and then it takes the sorted files as input, which is not correct, as indicated by Salmon developers:
" One of the fundamental assumptions of such inference methods is that observations (i.e. reads or alignments) are made “at random”. This means, for example, that alignments should not be sorted by target or position."(https://salmon.readthedocs.io/en/latest/salmon.html).
Thanks and best,
Alba
Command used and terminal output
Relevant files
No response
System information
No response