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griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
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why am I getting an "Error parsing inputs!(2)" error message when using regtools junctions extract? #150

Closed skalava23 closed 1 year ago

skalava23 commented 3 years ago

Hello,

I am running the following code:

for bamfile in ls run/geuvadis/*chr1.bam; do echo Converting $bamfile to $bamfile.junc samtools index $bamfile regtools junctions extract -a 8 -m 70 -M 500000 $bamfile -o $bamfile.junc echo $bamfile.junc >> test_juncfiles.txt done

This 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)

I have tried following the error message and adding the -s option to the code, but I still get the same error.

What is the reason behind this error message? I am using the example data for leafcutter and trying to convert .bam files to .junc files (this data has been used many times and worked for others). I downloaded regtools via conda for reference.

What could be going wrong? I would appreciate any insight. Thank you!

kcotto commented 3 years ago

I think all you need to do is put your BAM file ($bamfile) at the end after all of your options, including -o $bamfile.junc. Let me know if this works and if it doesn't, we can problem-solve more.

santataRU commented 1 month ago

I think all you need to do is put your BAM file ($bamfile) at the end after all of your options, including -o $bamfile.junc. Let me know if this works and if it doesn't, we can problem-solve more.

Thank you, Kelsy. I encountered the same issue, but your suggestion resolved it!