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Hi, I am running the latest cnvkit image on the docker hub.
I get spurious calls where many reads with mapq = 0. I tried cnvkit.py coverage with the -q option, but it does not do anything. Is this a …
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Hello,
I am trying to plot read coverage using kpPlotBAMDensity but I find large differences between chromosomes using this method. For instance, I run the code below.
```
custom.genome
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Hi, I am having hard time because it keeps giving me this error. I am sure about the paths for the bam files and I have tried it different ways and paths but still giving me this error. If you can p…
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Hi,
I am currently experiencing issues with the concoct_coverage_table.py file. I know that there is already entries for similar issues but none of them resolved my problem. I ran the split command (…
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what are issues and how to resolve this?
Thaks
RNS
I have got this error msg:
concoct_coverage_table.py contigs_10k.bed /media/majorram/Analysis_Data/singhrn/meta_assembly/mapping/s*.sorted.ba…
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## The need
I was profiling a bam file when I noticed that a massive amount of my reads were not used:
```
WARNING
====================================================
There were 553 reads pres…
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https://github.com/jipingw/DegNorm/blob/2e3e9c950849869289b8651f8c735aba4774cff5/R/coverage_cal_functions.R#L33
Should be
```
if(!file.exists(paste(bam_file_list[k],".bai",sep=""))){
```…
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Hi,
thanks for developing such an efficient and needed tool!
I have been looking around this and other repositories of ML4GLand to find examples of best practices to read a genome fasta and a ba…
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For the rule breadth of coverage to work, MaltExtract first has to run in order to generate the results/AUTHENTICATION/{wildcards.sample}/{wildcards.taxid}/MaltExtract_output/default/readDist/{wildcar…
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* Spladder version: 3.0.5
* Python version: Python 3.10.13
* Operating System: Mac
### Description
After running spladder build and spladder test without errors, I used spladder viz and ran in…