search

ClarkLaboratory / IsoLamp

Isoform discovery from long-read amplicon sequencing data
MIT License
2 stars 1 forks source link

where to specify path to BAMs #8

Closed domivika closed 3 months ago

domivika commented 3 months ago

Hello,

Another question I have is where to specify the path to BAM files if I already have them mapped and want to run isoform discovery modules as specified here:

# isoform discovery modules only (requires BAMs) IsoLamp -p params.ini -m isoform_discovery

My BAM files are stored in the same directories as FASTQ files.

Thanks!

domivika commented 3 months ago

Found it! I didn't notice it has to be finished with _primary_merged

function set_skip_mapping_vars() {

if ! test -f $OUTPUT_NAME/mapped_data/${OUTPUT_NAME}_primary_merged.bam then echo "No BAM file found, run mapping first." exit 1 fi

josiegleeson commented 3 months ago

Hi, yes this module assumes you've ran the mapping with IsoLamp... I might try and update the documentation so this is easier for future use.

But you're correct, the BAM file path will be: 'OUTPUT_NAME/mapped_data/OUTPUT_NAME_primary_merged.bam and it needs to be sorted and indexed.

Thanks!