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Comment: Creating loop for read groups using Picard
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ntsopoul
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try absolute paths
navigate to the directory with cd and use pwd to get the absolute directory.
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rheab1230
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Thank you. I will use this package since I am more familiar with R
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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…
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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
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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…
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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…
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You need to run bcftools index on your vcf file before running the suggested command.
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ntsopoul
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I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?
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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
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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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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?
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Afif Elghraoui
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Not in one step that I could find, but this works:
deletions:
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bcftools view --types indels --include 'ILEN<0' file.vcf | bcftools …
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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.
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