Aaron Quinlan comments

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                                            Aaron Quinlan

bedtools intersect fails when GFF file contains a ##FASTA section

You learn something new every day. Is it one entire section of ##FASTA or are such sections interleaved throughout the file?

bedtools intersect fails when GFF file contains a ##FASTA section

Hi Neil, The issue is the actual FASTA sequence line thereafter.

bedtools intersect fails when GFF file contains a ##FASTA section

Thanks Shaun. We won't be able to get a fix for this into the forthcoming release, but we will try to tackle it for the subsequent release. Thanks for pointing...

bedtools merge input too long

Can you provide a minimal example file and let us know what version you are using?

genomecov -d -pc -ibam showing no coverage for every position

The FLAG column in the examples you show is 255, which means that the read and its mate are unmapped (plug in 255 here: https://broadinstitute.github.io/picard/explain-flags.html). If all alignments are "unmapped"...

[segmentation fault] errors while converting coordinates to sequences using bedtools getfasta

could you give an example (ideally small) dataset that produces this issue?