User: abhilashtripathi10

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Posts by abhilashtripathi10

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Comment: C: Formatting BAM file and GTF file for feature counts
... Thank you for redirecting. ...
written 9 weeks ago by abhilashtripathi100
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Formatting BAM file and GTF file for feature counts
... I am trying to format the identifiers in my BAM file to match with the GTF file. I used Samtools: IdxStats tool on my BAM file and I got the following output: https://ibb.co/10rT9tL I am getting zero counts for RNA seq reads after using featurecount tool in galaxy. I suspect there is some problem w ...
alignment featurecounts rna-seq bam written 9 weeks ago by abhilashtripathi100
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Comment: C: Problem with recognizing adapters while using Cutadapt or Trimmomatic
... Thank you. I will take care of it next time. ...
written 11 weeks ago by abhilashtripathi100
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Problem with recognizing adapters while using Cutadapt or Trimmomatic
... I got my samples sequenced from a commercial facility. They used the following adapter sequences for sequencing Sample ID Index i7 Index i5 S0A GTTCTTCTGT CCAAGGTATT S0B CCAAGGTATT GTTCTTCTGT S0C TGTGGAGAGG AACGAACCGG S5A TTCCTTGAGG TGCTGT ...
rna-seq written 11 weeks ago by abhilashtripathi100 • updated 11 weeks ago by Ram32k
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Comment: C: Read length and sequencing depth for RNA-seq (for differential gene expression a
... Thank you for the suggestion. I am trying to be on the low end with more biological replicates as you suggested. ...
written 4 months ago by abhilashtripathi100
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Comment: C: Read length and sequencing depth for RNA-seq (for differential gene expression a
... Thank you for your suggestion. yes, because of budget constraints I am trying to go for 10-20million reads (50bp, SE)/sample. I have three biological replicates for each sample. ...
written 4 months ago by abhilashtripathi100
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Read length and sequencing depth for RNA-seq (for differential gene expression analysis) of bacterial RNA
... Hello Everyone My group in my lab wants to elucidate differential gene expression during bacterial biofilm growth on some material surfaces. For the same, I want to know what should be the minimum read length, total no. reads, and whether I should go for PE or SE RNA sequencing. I went through the ...
gene next-gen rna-seq sequencing written 4 months ago by abhilashtripathi100

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