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Hello developers,
Let me start by saying thanks for this awesome tool. Its been a lifesaver for me. But I do have a long winded question about how it calculates abundances, especially when it comes t…
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../RNAEditingIndex -d ../TestResources/BAMs/BAMs --genome hg38 -f _sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam
Error: Unable to open file ../TestResources/BAMs/BAMs/SRR5962217/…
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Dear Eager developer,
I found an error on converting vcf file from GATK ug with vcf2geome.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3280
at VCF2Genome.runUGAnalysis…
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Hello,
I was wondering if you were planning to add an option to use BAM files instead of SAM files for the coverage calculation ?
Or is there a way to retrieve the SAM content from STDOUT ?
I'm…
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Dear all,
I am using RiboDiPA 1.10.0 in R version 4.3.3, and when I run the wrapperFunction (RiboDiPA), it failed in the indexing step:
`Indexing`
`Data/Raw/RiboSeq/IMGN_B17/IMGN_B17_Riboseq_re…
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Needs to take capture kit into account.
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Hi, team.
I tried to use MAESTER(https://github.com/petervangalen/MAESTER-2021), and maegatk first.
But in my own data or test data cannot be processed, so i tried to mgatk test file.
Then i figure…
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I have come across an issue where velocyto crash when the number of reads aligned in a cell is very few. The velocyto matrix subsequently becomes empty.
If you want to run a bulk run this will break …
Xparx updated
5 years ago
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Hi,
We are looking to optimize the polishing step for reconstructing a plant genome using PacBio HiFi reads (Q30). Specifically, we tested both NextPolish and NextPolish2, followed by a variant cal…
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seem to have isolated it to this step:
minimap2 -a -t 2 -R "@RG\tID:run1\tSM:sample1\tLB:library1\tPL:ILLUMINA" refs/AF086833.fa reads/SRR1553425_1.fastq reads/SRR1553425_2.fastq | \
> samtools so…