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Thursday August 26 from 9 am - 11:30 PDT
Instructors:
Moderator: Marisa
Helpers:
Zoom link:
Description:
>This two hour workshop will introduce attendees to the slurm system for using, q…
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Does seq-lang work on windows or do I need to dual boot or put in a virtual machine for Linux to run this software?
If it works on Windows, is there a recommended way to install it? I can imagine d…
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As stated in the title. I tried the new gatk version 4.2.1.0 to update the GENCODE data for Funcotator.
Log:
/home/robby/Tools/NGS/gatk-4.2.1.0/gatk IndexFeatureFile -I /home/robby/Tools/NGS/genco…
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Hi, I am trying to run fragCount as follows:
`frag -b SP_1_N/SP_1_N.finalSorted.bam -w 1000 -d /srv/ngs/analysis/dalteriog/reference_genomes/hs/mapFiles -o SvABA_dir`
where `/srv/ngs/analysis/da…
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Sequenza is a tool for copy number variation analysis. Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R…
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Hello,
I have KO samples for an enzyme responsible for m6A modification, and I have identified many m6A sites in these KO samples. I am currently analysing the entire sample library to quantify m6A s…
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Discuss with Bob first.
The sequences are available in FASTQ format: https://ngdc.cncb.ac.cn/gsa/browse/CRA002522
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Hello
I have done paired-end sequencing and need to remove poly-A and poly-T sequences from R1 and R2 reads. Based on the manual, I ran this command:
fastp -x -i AH1_R1.fastq -I AH1_R2.fastq -o…
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I am having this problem using the SAM file to identify the off-target
python ~/bin/guideseq-1.0.2/guideseq/guideseq.py identify --aligned ~/Desktop/WORKS/CODE/download/AA_1.sam --target_sequence c…
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Total chromosome sizes are hardcoded in the function "macs2CallPeaksATACSeq" and "macs2CallPeaks" of ngstk.py. So I ran into problems when I did the analysis with mm9. Maybe this could be added to the…