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Hey Everyone, For `nf-core/rnasplice` pipeline, h...
# rnasplice
m
Hey Everyone, For 
nf-core/rnasplice
pipeline, has anyone ran it with using “Salmon quantification files” instead of FASTQ ones: https://nf-co.re/rnasplice/1.0.4/docs/usage/? I can run FASTQ ones just fine. But, when using “Salmon quantification files” format, I’m getting into this error, even though I'm not planning to use FASTQ files as input:
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Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (mouse_liver_2.csv)'

Caused by:
 Process `NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (mouse_liver_2.csv)` terminated with an error exit status (1)


Command executed:

 check_samplesheet_fastq.py mouse_liver_2.csv samplesheet.valid.csv
 cat <<-END_VERSIONS > versions.yml
 "NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK":
     python: $(python --version | sed 's/Python //g')
 END_VERSIONS

Command exit status:
 1

Command output:
 (empty)

Command error:
 [CRITICAL] The sample sheet **must** contain these column headers: fastq_1, fastq_2, condition, sample, strandedness.

Work dir:
 /home/tud03125/pipeline/mouse_liver_rnasplice_2/work/76/d85d34d19e1180ad36d1539d298892

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Just in case, my input samplesheet looks like this:
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sample	salmon	strandedness	condition
I1	/home/tud03125/mouse_liver_rnasplice/salmon/I1	reverse	FASTED
I2	/home/tud03125/mouse_liver_rnasplice/salmon/I2	reverse	FASTED
I3	/home/tud03125/mouse_liver_rnasplice/salmon/I3	reverse	HCD
I4	/home/tud03125/mouse_liver_rnasplice/salmon/I4	reverse	HCD
I5	/home/tud03125/mouse_liver_rnasplice/salmon/I5	reverse	HCD_MK2206
I6	/home/tud03125/mouse_liver_rnasplice/salmon/I6	reverse	HCD_MK2206
I7	/home/tud03125/mouse_liver_rnasplice/salmon/I7	reverse	HCD_MK2206
I8	/home/tud03125/mouse_liver_rnasplice/salmon/I8	reverse	HCD_MK2206
I9	/home/tud03125/mouse_liver_rnasplice/salmon/I9	reverse	HCD_SPHINX31
I10	/home/tud03125/mouse_liver_rnasplice/salmon/I10	reverse	HCD_SPHINX31
I11	/home/tud03125/mouse_liver_rnasplice/salmon/I11	reverse	HCD_SPHINX31
IA1	/home/tud03125/RNAseq/salmon/fasted_rep1.tar.gz	reverse	FASTED
IA2	/home/tud03125/RNAseq/salmon/fasted_rep2.tar.gz	reverse	FASTED
IA3	/home/tud03125/RNAseq/salmon/fasted_rep3.tar.gz	reverse	FASTED
IA4	/home/tud03125/RNAseq/salmon/highcarb_rep1.tar.gz	reverse	HCD
IA5	/home/tud03125/RNAseq/salmon/highcarb_rep1.tar.gz	reverse	HCD
IA6	/home/tud03125/RNAseq/salmon/highcarb_rep3.tar.gz	reverse	HCD
t
Well, the column with the Salmon results should be called 
salmon_results
(no guarantee this will work, I have never use that). As a side note, be aware that Salmon is based on known (annotated) transcripts, so you won't (by definition) find anything beyond those and miss out on any novel splice junctions or transcripts, which tools may be able to detect if you start from FASTQs.
👍 1
m
@Thomas Danhorn Got it. What about Genome or Transcriptome BAM files as inputs? Have you done that before? Can you comment on it, please?
t
No, I don't do a lot of splicing, and I have only started from FASTQs. Genome BAMs should give you all options, but with transcriptome BAMs you are again locked into the alternative splicing options that are provided by the annotation used to make the transcriptome file against which the reads were aligned to make the BAM.
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