regtools Error ：Please supply strand specificity with '-s' option!

[geng-lee]

regtools Error ：Please supply strand specificity with '-s' option!

for bamfile in `ls Bam/*.bam`; do
    echo Converting $bamfile to $bamfile.junc
    samtools index $bamfile
    regtools junctions extract -a 8 -m 50 -M 500000 $bamfile -o $bamfile.junc 
    echo $bamfile.junc >> juncfiles.txt
done

[jackhump]

hi, sorry for the delay. Which version of regtools are you using?

[safelker]

I am having the same issue and I am using regtools 0.6.0, for what its worth

note: this is just working with the example data provided in the differential splicing tutorial

[hkmztrk]

@geng-lee @safelker I'm getting the same error with regtools 0.5.2, how did you proceed?

[goldenflaw]

You should use the -s flag with the appropriate setting depending on your RNA-seq library.

Best, Yang

On Wed, May 19, 2021 at 8:41 AM hkmztrk @.***> wrote:

@geng-lee https://github.com/geng-lee @safelker https://github.com/safelker I'm getting the same error with regtools 0.5.2, how did you proceed?

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[skalava23]

Has anyone figured out how to solve this error? I'm running into a similar issue, where I either get the "Please supply strand specificity with '-s' option!" error, or the "Error parsing inputs!(2)"

@jackhump the version of regtools is 0.5.2

There is the message that pops up: Converting run/geuvadis/RNA.NA06985_CEU.chr1.bam to run/geuvadis/RNA.NA06985_CEU.chr1.bam.junc

Program: regtools Version: 0.5.2 Usage: regtools junctions extract [options] indexed_alignments.bam Options: -a INT Minimum anchor length. Junctions which satisfy a minimum anchor length on both sides are reported. [8] -m INT Minimum intron length. [70] -M INT Maximum intron length. [500000] -o FILE The file to write output to. [STDOUT] -r STR The region to identify junctions in "chr:start-end" format. Entire BAM by default. -s INT Strand specificity of RNA library preparation (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR). REQUIRED -t STR Tag used in bam to label strand. [XS]

Error parsing inputs!(2)

Any insight would be appreciated! Thank you