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First of all, great tool.
pyGenomeTracks --version
python --version
`pyGenomeTracks 3.8`
`Python 3.10.12`
When I have a configuration file with one bed graph with max_value set to auto I get …
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If I have multiple bam files (replicates), how ```bamCoverage``` work?
There used to be a function ```multiBamCoverage``` but it has been removed from the latest deeptools (3.5.5).
How do you sugges…
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Hi,
I am trying to run reptile on pre-trained model mm_model_coreMarks.reptile using methylation data. Is there any issue with bw generation, I have methylation base call bed files containing chr no,…
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First of all, let me say that I was shocked to see how fast this tool works. Being able to obtain all RefSeq's gene coverage information from a 30X human WGS sample in less that 1 minute was really im…
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Thank you for keeping things organized! I was able to download the resource files following the instructions. After browsing the files included, I have a couple of questions regarding the following fi…
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When working with stranded, paired end RNA-seq, ALFA does not correctly report reads on categories.
# Example
I copied the supplied `quick_start.chr_len.txt`,`quick_start.gtf` and `quick_start.…
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Hi,
thank you for the useful tool! I just have one question on this part:
**3.pseudo-code for generation of bigwig files from a bed file
libSize=`cat sample1.bed|wc -l`
scale=15000000/($libSize*$S…
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When running 2.0_Dogatcher.py, I get the following error :
Traceback (most recent call last):
File "Dogcatcher/2.0_Dogcatcher.py", line 896, in
last_time = time.time()
File "/opt/conda…
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Hi,
i am running the make_view point script.
Genome: mm10!
One track in the bedgraph file looks like this:
track type=bedGraph name='hicpro HIC_chr11_291356' description='hicpro HIC_chr11_2913…
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Dear all,
I would like to know if there is a way to properly visualize methylation information obtained from modkit in IGV genome browser (testing IGV 2.17 snapshot).
In particular, I ran Dorado wit…