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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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program failed #98

Closed lmanchon closed 1 year ago

lmanchon commented 1 year ago

--Hi, the program failed with: Genrich -t DGV_chr20.bam -c chr20.bam -o DGV_chr20_hg38.peaks -f DGV_chr20_hg38.log -q 0.05 -a 20.0 -v

Processing experimental file #0: DGV.bam BAM records analyzed: 5751753 Paired alignments: 0 Unpaired alignments: 5751753 secondary alns: 420303 Fragments analyzed: 0 Full fragments: 0 Error! Experimental sample has no analyzable fragments

my experimental bam contains only 50bp single-end reads.

thank you --

jsh58 commented 1 year ago

Genrich analyzes only paired alignments by default, as described here and also #8 and #24. For single-end reads, you must specify either -y or -w <int>.