User: ningyuan.sg

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Posts by ningyuan.sg

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Comment: C: salmon NumReads inconsistent with depth from --writeMappings?
... 1. Frankly, I've just heard of `tximport`. Obviously, I should be using that, but... I think the apparent discrepancy between maximum read depth and TPM still hold, even if we are looking at a transcript rather than gene level. 2. `samtools 1.9`, `Using htslib 1.9`. No, I do not pass any option to ` ...
written 12 days ago by ningyuan.sg0
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Comment: C: salmon NumReads inconsistent with depth from --writeMappings?
... Thank you. I obtained the MaxDepth column by using `samtools depth -r `, where is the indexed and sorted file output by `salmon ... --writeMappings=`. [1] Columns are combined with a simple R script [2]. In my next step, I use `edgeR` to import gene counts in `quant.sf` using the first and fourth ...
written 12 days ago by ningyuan.sg0
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Comment: C: salmon NumReads inconsistent with depth from --writeMappings?
... I understand your explanation, but I have some doubts as to the likelihood that this difference would cause such a counterintuitive and drastic difference in read depths. Thank nonetheless, though. ...
written 14 days ago by ningyuan.sg0
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Comment: C: Selecting Random Pairs From Fastq?
... Yes, that is correct. The seed only affects how the reads are selected. ...
written 14 days ago by ningyuan.sg0
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Comment: C: salmon NumReads inconsistent with depth from --writeMappings?
... Sure, but wouldn't their maximum read depths be *roughly* proportional to their TPM? ...
written 14 days ago by ningyuan.sg0
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salmon NumReads inconsistent with depth from --writeMappings?
... I am trying to count gene expression for differential expression analysis. I used salmon to quantify genes against a reference transcriptome to get their TPM, but also --writeMappings to check their max read depth. I got: Name EffectiveLength TPM NumReads MaxDepth NR_1 ...
software error R salmon samtools rna-seq written 16 days ago by ningyuan.sg0

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