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The coverage across most of the sites specified in the given BED file is extremely low, typically 10 or less.
This is not always true, as some regions are extremely saturated.
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```
WARNING:toil.leader:The job seems to have left a log file, indicating failure: 'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' v/5/jobJt9k…
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Hi @Wesserg - After reading your recent publication in Computational Biology and Chemistry, I'm interested in applying SRSFseq to RNA-seq data where I'm expecting clear (but relatively small) differen…
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Currently, JBrowse allows for the back-end configuration and setup of combination tracks in the form of BAM / BigWig, such that users can select to show both a BAM file's aligned RNA-seq reads or BigW…
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Hello, I am having trouble getting bcftools to call the ALT allele with 61 DP4 depth, it instead is only showing the REF call with 0 DP4 read depth.
The ALT call is correctly identified in the 'bc…
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Hi, @abhijitcbio
When I follow step1 of HiCnv software, I found that `F_GC_MAP.file.sh` script needs `MultiTrackMappability.bw` file. However, only `Mappability` file of human, mouse and some mode…
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Hi there! Thank you for developing this powerful tool, I've been having a lot of fun with it.
I have a question about the inStrain compare SNV pooling outputs. I've run inStrain profile on 21 samp…
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Hello,
I'm using CuteSV on Nanopore data with 30X coverage. My sample has a known duplication that isn't making it into the final output but it is detected in the signatures file. I was wondering i…
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Dear,
I used Lumpy via Smoove to call CNVs in a population of ~600 samples.
First, I used 200 high coverage samples to discover CNVs, and then genotyped the sites in the entire population.
In t…
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Hi sir,
here is my coding
` python /data1/work/software/AmpliconArchitect/src/AmpliconArchitect.py --bam bam/YX150000261T.final.bam --bed gain.bed --out AA_out`
it keeps running for 60h but no outp…