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Answer: Fastqc report analysis
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Comment: Fastqc report analysis
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npavliukovec
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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
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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
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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
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ntsopoul
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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
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Joana
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You need to run bcftools index on your vcf file before running the suggested command.
Comment: Fastqc report analysis
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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
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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
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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…
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Pierre Lindenbaum
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duplicate of https://www.biostars.org/p/9558127/
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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…
Answer: Need help teasing out insertions and deletions with bcftools stats file.vcf > fi
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Afif Elghraoui
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Not in one step that I could find, but this works: deletions: ``` bcftools view --types indels --include 'ILEN<0' file.vcf | bcftools …
Comment: How to add gene information below the BSmooth result ?
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diqixiaoyaoer
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Thank you, sir. I have looked into your thesis. It's really great. I may have a try on Gviz if I don't have any idea about my question.
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
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rackbersingh
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Brilliant, thanks for the advice, i think after looking into what the community has said I have invested into learning the groovy language …
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Juke34
7.7k
Change merge_loci to true
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igor
13k
The addition of mouse-specific pathways to MSigDB is relatively recent. The package has not been updated to incorporate the latest version …
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