Open adamrtalbot opened 10 months ago
@adamrtalbot could you supply the exact data sets you used to run ReSeq? And the command you used, if that's possible :)
I'm afraid it was at an old job. It should work with any 'normal' BAM as I remember.
OK I managed to get it working with the test data files but I had to use the flag --adapterFile TruSeq_single
to disable adapters!
OK, an additional thing I had to add was the coverage (-c
). With the homo_sapiens data:
reseq illuminaPE \
--verbosity 4 \
-j 4 \
-r genome.fasta \
-b test.paired_end.sorted.bam \
-c 1 \
--adapterFile TruSeq_single \
-1 test.1.fastq.gz \
-2 test.2.fastq.gz
Nextflow process will look something like this for paired end data:
reseq illuminaPE \\
${args} \\
-j ${task.cpus} \\
-r ${fasta} \\
-b ${bam} \\
-1 ${prefix}.1.fastq.gz \\
-2 ${prefix}.2.fastq.gz
Genome: file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
Index: file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
BAM: file(params.modules_testdata_base_path + genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam, checkIfExists: true)
Awesome, thank you
Trying to solve https://github.com/schmeing/ReSeq/issues/23
Is there an existing module for this?
Is there an open PR for this?
Is there an open issue for this?
Are you going to work on this?
Assignees
to facilitate tracking who is working on the module