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A: Fold change - a final explanation
Comment: scRNA-seq quality control
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
Answer: Genes' fpkm values through cufflink
Answer: Genes' fpkm values through cufflink
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Recent Replies
Comment: Z score
by
Akash D
▴ 40
Ok. However, if i perform it on log2FC, there wont be any control samples visible in my heatmap. Your answer is perfect.
Comment: Z score
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ATpoint
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You can apply Z-scores on whatever you want, but it must make sense and depends on what you want to do. What is the context? See for exampl…
Answer: Z score in RNAseq
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Akash D
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Can Z score be applied on log2FC and then visualized? Alternatively, Can log2FC be converted to Z scores and then visualized as heatmap?
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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ATpoint
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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…
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
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colindaven
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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?
by
anikcropscience
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Ok, thank you for the reply. I will check out the DP field then.
Comment: Alternatives To Liftover
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Thanujay S
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Hey! Would you consider building an API for the same? Is that something you have planned?
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
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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…
Comment: samtools write-index
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LucisTheFather
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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
by
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-…
Comment: samtools write-index
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LucisTheFather
• 0
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…
Comment: Which 1000 genomes 30x files should I use for imputation?
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Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
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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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Jeremy
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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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GenoMax
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Past thread: https://www.biostars.org/p/178266/
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