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coverageBed coverage/number of features discrepancy

1

Hello, I am running coverageBed to determine coverage of a specific regions of a genome by RAD tag data (restriction-site associated DNA reduced representation sequences). I am interested in the...

ghost

arq5x

https://groups.google.com/forum/?fromgroups=#!topic/bedtools-discuss/_Pinr6dLG1E While closest doesn't do this in one fell swoop, it should be able to do it in two steps via -D, -id, and -iu. However, I cannot get a...

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Controlling delimiter in -nms option of mergeBed

4

I use `mergeBed` frequently with the `-nms` feature to list multiple transcripts that BED intervals belong to, e.g.: ``` chr1 3195981 3197398 ENSMUST00000162897;ENSMUST00000159265 - chr1 3203519 3207049 ENSMUST00000159265;ENSMUST00000162897;ENSMUST00000070533 - ```...

yarden

Support for remote files.

1

Self explanatory. Use curlib? boost::asio? We would prefer to not use boost::asio in order to minimize external dependencies. Is there a stable C++ library for reading remote files?

arq5x

Add a 'flip' tool.

6

Like bit flipping, this would flip the strand of every interval.

arq5x

Instead of providing genome (-g) files, have chrom_sizes for several widely-used genomes burned into the tool. Obvious issue is chromosome naming schemes. Could have: ``` 'hg19' [chr1, chr2, ...] 'hg19-int'...

arq5x

https://groups.google.com/forum/?fromgroups=#!topic/bedtools-discuss/9cD2Er4wFps

arq5x

https://groups.google.com/forum/?fromgroups=#!topic/bedtools-discuss/2UzYJ7hMk_0

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Istvan Albert pointed out that when an error is encountered, bedtools currently prints the error following by the help. This forces the user to have to scroll up quote a...

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