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updated 14 hours ago by Ram 38k • written 8.0 years ago by fiochettal ▴ 10

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Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories With Just One Command?

Comment: samtools idxstats not removing ChrM

The Biostar Handbook. A bioinformatics e-book for beginners.

Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)

Comment: GATK GenotypeGVCFs explain

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Comment: GATK GenotypeGVCFs explain by Pierre Lindenbaum 153k

https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists

Comment: GATK GenotypeGVCFs explain by Sarah ▴ 30

thank you

Comment: GATK GenotypeGVCFs explain by raphael.B ▴ 270

It limits the operation to some genomic regions given as parameter

Comment: GATK GenotypeGVCFs explain by Sarah ▴ 30

what does the option L

Comment: GATK GenotypeGVCFs explain by Pierre Lindenbaum 153k

GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.

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CpGs may be annotated to more than >1 gene simply because gene regions overlap on the genome. If you want to associate each gene to a me…

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Please give a look to [this post][1] for increasing the probability to get an answer. If I may add some needed info: 1. What exactly do y…

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Wow, thank you so much for your explanation! My conda channel is indeed set to strict priority. Should packages with different dependencie…

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You can use BioMart to convert your "gene-IDs" to gene symbols, but you need to specify from which database your gene identifiers come from

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If you search "DAVID dotplot" on this forum, you have many answers to your question. Note that you can also perform DAVID Functional Enrich…

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nottested, something like: ``` version 1.0 workflow BIOSTAR { call FIRST { } scatter (F in FIRST.each_F)…

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You can try https://genebe.net , it is similar to Varsome though...

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Hi, free ACMG implementation without restrictions can be found at https://genebe.net . AFAIK there is also a free API coming.

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I don't have the data available. I want to identify such datasets. The overall aim is to determine what factors influence fastq data qualit…

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I don't know what exactly the error message means. What I can tell you is that a burn-in of 2500 generations is absolutely inadequate. That…

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