gabed

Can't generate coolerfile with cload at very high resolution (200/400bp)

1

Hi, I am having some trouble running cload at higher resolutions (eg 200/400bp). The output freezes at the first batch of chromosomal locations and doesn't continue, even when run for...

How is fragment length calculated?

1

Hi, I am using some BAM files which have been mapped and then processed into a list of 1-bp coordinates with strand information, i.e: chr4 3648 - - Currently, I...

AlignmentSieve returns empty bam file

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Hi, I am trying to use alignmentSieve to shift some reads in a BAM file. I am trying the following command using deeptools 3.5.0: alignmentSieve -b sorted.test.bam -o sieve.sorted.test.bam --shift...

alignmentSieve seems to not be working

2

Hi everyone, since I was having a challenge shifting reads manually and using deeptools, I decided to shift reads with alignmentSieve. In this, I truncated a bam file to the...

bamtobed --> shifting --> bedtobam seems to not work with bamCoverage

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Hi there, I am shifting some reads for nucleosome analysis. Currently, I use bamtobed to create a bed file, I shift this using custom scripts, then I use bedtobam to...

Q: How exactly does cutoff-analysis work?

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Hi, I am using --cutoff-analysis to see where to put my p-values in combination with IDR. I am confused, because I called peaks with default settings: macs2 callpeak -t ${files[@]}...

Q: How to identify sub-peak / summit width?

2

Hi, I am calling peaks with MACS2 using: `macs2 callpeak -t reads.bam --call-summits -c input.bam -B --outdir peaks ` Since some of the peaks have subpeaks, MACS will call summits...

Which coordinates does pairix return?

3

For example, let's say the .pairs output is: READID chrX 16145203 chrX 16213822 + - UU Is 16145203 the left-most or the right-most coordinate on this read? Likewise for 16213822?...

Trained on mouse?

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Is there a pre-trained DNA BERT trained on mouse genome? Thanks very much, Gabe

Add opacity?

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Is it possible to add opacity to the chord plots?