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Comment: How to get the ratio of allele counts from GATK derived VCF file?
Setting up Aspera Connect (ascp) on Linux and macOS
Setting up Aspera Connect (ascp) on Linux and macOS
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Answer: Genes' fpkm values through cufflink
Genes' fpkm values through cufflink
Error when looping over multiple columns in a data frame in R
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Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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Just for comparison, I deal with scRNA-seq daily and my workstation is a 12700k i7 with 128GB RAM and even this is actually more than I nee…
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- As others have said, 1-2 workstations are probably the way to go. - A Linux OS like Ubuntu is probably easiest and has best docs - RA…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
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anikcropscience
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Ok, thank you for the reply. I will check out the DP field then.
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Hey! Would you consider building an API for the same? Is that something you have planned?
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20k are good money for some workstations ... probably you need to run more samples at the same time ... for some 1000s you could take a wor…
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``` -o alignment.sorted.bam##idx##alignment.sorted.bam.bai ``` This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index
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LucisTheFather
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Really appreciate your help Pierre! I am a little bit confused btw. do you mean this: ``` rm -vf alignment.sorted.bam.bai minimap2 -ax map-…
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Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests) and none of…
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The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
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First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
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Past thread: https://www.biostars.org/p/178266/
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Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
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Here is the [RatGTEx][1] [1]: https://ratgtex.org
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Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
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