ERROR run from bam

[QuanlongJiang]

Hi,
I ran the program using BAM files and encountered the following error. It seems that the program did not process the BAM files correctly. Could you please provide a more detailed explanation of how to use the BAM files to generate the data?

Thinks!

[bingqiWu]

Hi, I ran the program using BAM files and encountered the following error. It seems that the program did not process the BAM files correctly. Could you please provide a more detailed explanation of how to use the BAM files to generate the data?

Thinks!

@QuanlongJiang
Hi, I meet same problem.
Did you solve it?

[xiaobearxiaobear]

@bingqiWu @QuanlongJiang
Hi, I meet same problem.
Did you solve it?

[ch31lyDim]

Same issue

[jettmcp]

Same here

[brandon-hastings]

The error is due to not having a path to your junction files associated with the bam files. If using STAR alignment, these are usually generated automatically. If using minimap, you can create BAM files using the leafcutter scripts. I got errors in this step as well, and ended up needing to use bedtools bamtobed -bed12 file.bam to generate the initial bed file, then leafcutter/bed2junc.pl new_file.bed new_file.junc.
Do this for each bam file if necessary, put them all in a directory (e.g., junction/) and then put that directory path in the srr.yaml file before running the program.
Not sure if leafcutter should run automatically in the absence of junction files since this was unclear for me in the documentation, but it does not for me. Also it's best to use bedtools bamtobed function rather than the original leafcutter bam2junc.sh file included in this repository, as this produces an error currently.

[Melody020311]

This SCASL version expects process.junction to exist and contain junction files.
If the junction directory is missing/empty, SCASL cannot build the junction matrix.
Generating junctions from BAM also requires working leafcutter + samtools.

Generate junction files from split BAMs first (parallel), then set process.junction to that folder:

BAMDIR=/path/to/bam_by_barcode_split
JUNCDIR=/path/to/junction_by_barcode
LCDIR=/path/to/SCASL/leafcutter

mkdir -p "$JUNCDIR"

find "$BAMDIR" -maxdepth 1 -type f -name "*.bam" -print0 \
| xargs -0 -n1 -P16 -I{} bash -c '
  bam="{}"
  base=$(basename "$bam" .bam)
  out="'"$JUNCDIR"'/${base}.junc"
  [[ -s "$out" ]] && exit 0
  bash "'"$LCDIR"'/bam2junc.sh" "$bam" "$out"
'

YAML:

process:
  junction: /path/to/junction_by_barcode/