User: nanoide

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nanoide10
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Posts by nanoide

<prev • 22 results • page 1 of 3 • next >
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Comment: C: TPKM vs FPKM
... Thank you, now I think I got a pretty good idea that is not a common term, I'll make sure to recheck where my data's coming from. Thanks! ...
written 7 weeks ago by nanoide10
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Comment: C: TPKM vs FPKM
... I am aware of the differences between FPKM/RPKM and TPM. I had never heard of TPKM either. It seems it's used by some few papers. For example, [this][1] scholar search. I would say it's used as FPKM but I wanted to be sure. [1]: https://scholar.google.es/scholar?hl=es&as_sdt=0%2C5&q=tpk ...
written 7 weeks ago by nanoide10
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Comment: C: TPKM vs FPKM
... Thanks for the source, it's alway good to refresh these concepts ...
written 7 weeks ago by nanoide10
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TPKM vs FPKM
... Hello, so I have a simple question I hope anyone can clarify I've seen some papers presenting RNA-seq data in TPKM, but I'm not sure on what does this mean. Is this the same than FPKM? Thanks for your time ...
fpkm rna-seq written 7 weeks ago by nanoide10 • updated 7 weeks ago by ATpoint11k
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Comment: C: How to get regions with mapped reads
... Thank you very much, I think bamToBed worked for my purpose here ...
written 9 weeks ago by nanoide10
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Comment: C: How to get regions with mapped reads
... Thank you for your help, I will do it next time ...
written 9 weeks ago by nanoide10
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How to get regions with mapped reads
... Hello all, So I would like to get the sequence of the genomic regions with mapped reads after an RNA-seq analysis. First, I have mapped the reads into a reference genome using hisat2 and `--rna-strandness F`. Does anyone have a suggestion on how I could extract the regions of the genome with ma ...
bedtools bed file rna-seq bam file written 9 weeks ago by nanoide10 • updated 9 weeks ago by RamRS19k
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Comment: C: Ovation RNA-seq system, bionfomatic alignment and htseq-count
... Will do. Thank you both ...
written 9 weeks ago by nanoide10
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Comment: C: Ovation RNA-seq system, bionfomatic alignment and htseq-count
... Thank you so much for your clarifying response. I have inherited some code where they first mapped using hisat2 and --rna-strandness F and then performed conts using htseq-count and --stranded reverse. Then this combination is not correct right? Thanks for your time ...
written 9 weeks ago by nanoide10
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Ovation RNA-seq system, bionfomatic alignment and htseq-count
... Hello, We have used ovation RNA-seq system and prepared some libraries. We have sequenced single-ends. We want to use hisat2 and htseq counts to get counts per gene in our organism. I wondered if someone has worked with this before, what parameter should be specificied in rna-strandness on HISAT2 p ...
htseq-count rna-seq hisat2 written 9 weeks ago by nanoide10 • updated 9 weeks ago by caggtaagtat380

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