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With large datasets and limited disk capacity, saving intermediate fastq files as raw fastq may take up hundreds of GBs of disk space. Disk usage may be decreaused by using gzipped fastq files. The to…
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Hello, I was trying to use your BindingSiteFinder and got an error:
Error in if (all(!df.global$increaseOverMin)) { :
missing value where TRUE/FALSE needed
I was using BSFind(object = KObds…
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Hello,
I wanted to ask if there is a way with vcfanno to annotate a variant with its proximity to a certain feature. Specifically, I would like to know if a variant is close to the intron/exon bounda…
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Hi,
When I apply bamtofastq to a bam file (illumina single-end reads aligned with STAR), I do get duplicated reads in the fastq.
Checking the former version - 2.29.2 - it works as expected (with…
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```
Users have requested wrappers to use BEDTools from within Galaxy.
```
Original issue reported on code.google.com by `aaronqui...@gmail.com` on 4 Jul 2010 at 9:24
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Hi
I am currently working on ATAC data from PE sequencing. When I called peak with following command:
`macs2 callpeak -t my_sample.bam -f BAM --nomodel -g hs -n name -q 0.05 --extsize 200 --shift -…
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Currently -f applies (confusingly) to the -bed file.
https://groups.google.com/forum/#!topic/bedtools-discuss/hzRnjQfhyZM
arq5x updated
4 years ago
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I am using the following code to add flanks upstream of sequences while taking strand into account:
```
>bedtoolsr::bt.flank(i = ApalmGFF3, g = sequenceLengths, l = 1000, r = 0, s = TRUE)
data …
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`shift` should move an interval left or right by either a fixed number of bases or a specific fraction of a chromosome.
arq5x updated
10 years ago
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I have encountered some bugs and failed to run them on several machines. The first problem is the dynamic library, but this is not the main problem. You can see the difficulties encountered in running…