User: Asad Prodhan

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Posts by Asad Prodhan

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Comment: C: ballgown and pData
... Thanks Morris. Now, I am using DESeq2 instead of Ballgown. My RNA-Seq workflow is HISAT2 - StringTie -DESeq2. It seems to be working fine. To help others running into the same issue, here I present what I am doing: I have estimated transcript abundance with the following call. stringtie –e ...
written 26 days ago by Asad Prodhan0
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Comment: C: ballgown and pData
... Hi Morris, I am using HISAT2 - StringTie -Ballgown pipeline. I was wondering if you could please comment on the following error message? Thanks. bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "PC", pData=pheno_data) > Sat Jul 11 09:24:49 2020 > Sat Jul 11 09:24:49 2020: Read ...
written 4 weeks ago by Asad Prodhan0
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Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
... **A 'bcftools' script for:**  Extracting SNP data from GBS data in vcf file format  Filtering out raw SNPs to a usable set of SNPs **I. Extracting the headers:** `bcftools view -h input_file.vcf.gz | awk '/CHROM/{print}' | cut -f 1-5,10- > output_file_header.txt` > h, headrer; ‘awk’ ...

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