User: akibio

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akibio0
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Posts by akibio

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Comment: C: I have aligned reads and gene counts from STAR. How should I calculate TPM from
... This is very helpful. So by using gffread, I can obtain a transcriptome fasta and using this I can essentially align my reads to the transcriptome using Kallisto or Salmon? And both can estimate raw counts and normalized counts? This would reduce computation time by a lot! ...
written 8 days ago by akibio0
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Comment: C: I have aligned reads and gene counts from STAR. How should I calculate TPM from
... Thanks! Since I don't have a fasta file of the transcriptome of my organism, I don't think I can use Salmon. Is that correct? ...
written 8 days ago by akibio0
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I have aligned reads and gene counts from STAR. How should I calculate TPM from these?
... Hi all, I have aligned reads from STAR with `--quantMode TranscriptomeSAM GeneCounts`, which then outputs the files `Aligned.out.sam` `Aligned.toTranscriptome.out.bam` and `ReadsPerGene.out.tab`. I'd ideally like a piece of reputable software to calculate the TPMs from these files (plus any necess ...
rna-seq written 9 days ago by akibio0 • updated 9 days ago by ATpoint40k
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Comment: C: [Prokaryote] How to go from reads to counts given that there is no exon column i
... Thanks, this then may be a silly question but does featureCounts require the exon column? Also, I initially chose to use STAR since it is provably far faster than any other aligner, however I wonder if prokaryotic organisms ever see this benefit. ...
written 14 days ago by akibio0
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[Prokaryote] How to go from reads to counts given that there is no exon column in gtf file?
... I am trying to go from raw reads to counts and then to TPM/TMM values of gene expression for a prokaryotic organism (via mapping the RNA sequencing reads to the reference genome). I have read that an annotation file (gtf or gff3) is needed, and encountered this issue firsthand when STAR threw an err ...
alignment rna-seq written 14 days ago by akibio0 • updated 14 days ago by Juke344.8k

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