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Answer: Problem generating a .vcf after upgrade of samtools and bcftools

Answer: RPKM and FPKM quality control check and filtration

A: Decoy In Reference Assembly

A: Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File

Comment: Plot in R: Presence of bacteria type A vs bacteria type B in different groups

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Answer: Problem generating a .vcf after upgrade of samtools and bcftools by Andy • 0

Really the only needed, that help worked, thank's

Comment: Active enhancers for mm39 by seidel 11k

Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…

Comment: Creating loop for read groups using Picard by ntsopoul ▴ 20

try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.

Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140

Thank you. I will use this package since I am more familiar with R

Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140

thank you. i will go through it

Comment: Fastqc report analysis by npavliukovec • 0

Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…

Comment: My fastq files(paired end) have different read number by kimgeng • 0

Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…

Answer: My fastq files(paired end) have different read number by ntsopoul ▴ 20

Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…

Answer: Can I use abundance from Tximport to compare the expression level of transcript by ntsopoul ▴ 20

No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…

Comment: Easy way to split VCF file by chromosome by Joana • 0

You need to run bcftools index on your vcf file before running the suggested command.

Comment: Fastqc report analysis by ntsopoul ▴ 20

I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?

Comment: Fastqc report analysis by npavliukovec • 0

Thanks for your answer, it really helped me. Also, I added --illumina options, because then I checked MultiQC report for all of my samples …

Answer: Fastqc report analysis by ntsopoul ▴ 20

Hi there, Cool that you learn to do these things and welcome to the bioinformatic community. In my opinion, both of the reports look to h…

Comment: Creating loop for read groups using Picard by Pierre Lindenbaum 153k

duplicate of https://www.biostars.org/p/9558127/

Comment: ClusterProfiler enrichKEGG – remove organism name in plots? by Mensur Dlakic ★ 23k

Is there a problem in using program version that produced your top plot? Unless there is known bug in a program, or a super-useful feature…

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