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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...

gdolsten

AlignmentSieve returns empty bam file

1

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...

gdolsten

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...

gdolsten

`NaN` in computeMatrix

1

Hi there, thank you for developing deeptools. I have a question. I have a small number of `NaN` in the output file (`-o`) of `computeMatrix reference-point`. Where do they come...

markgene

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

2

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...

gdolsten

Is TSS enrichment plot showing the correct output?

1

**Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :** - [x] Search whether this issue (or a similar issue) has been...

kkupkova

computeMatrix time cost

1

Hi, Do you have an estimate on how the time cost for computeMatrix scales with -R? I have a bed with 825510 entries and I could threshold that to a...

diazlab

The names of the regions are the first column names in the header. The issue seems to be because of a missing `info = []` above this line: https://github.com/deeptools/deepTools/blob/ac42d29c298c026aa0c53c9db2553087ebc86b97/deeptools/heatmapper.py#L981 This...

marcoct

**Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :** - [x] Search whether this issue (or a similar issue) has been...

joncahn

PlotProfile - Heatmap controversy

5

**Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :** - [ ] Search whether this issue (or a similar issue) has...

ANDdna1991