User: Tania

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Tania10
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Posts by Tania

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Comment: C: How low is too low mapping to proceed with differential expression analysis?
... I use blat, they are human samples. Could this be related to tumor issues? Those 2 problematic samples are human tumors. You mean, I switch to BBMap then edgeR? ...
written 1 day ago by Tania10
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Comment: C: How low is too low mapping to proceed with differential expression analysis?
... I was checking insert sizes to see if adapters go through reads. I am still not sure how bad my insert sizes distribution is affecting the mapping. But fastqc shows no adapters, so I think of moving forward for now. I worked on finding the rRNA inclusion, as mentioned in this post, it jumps from 3% ...
written 1 day ago by Tania10
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Comment: C: How low is too low mapping to proceed with differential expression analysis?
... Thanks Devon, much appreciated. ...
written 1 day ago by Tania10
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Comment: C: How low is too low mapping to proceed with differential expression analysis?
... **Thanks Devon so much.** Any hint how can I find if it is enriched in pre-mRNA or not? Like using STAR, what can I see to make the conclusion it is pre-mRNA enriched? ...
written 1 day ago by Tania10
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How low is too low mapping to proceed with differential expression analysis?
... **Hi Everyone** When I used a comprehensive transcript `gencode.v27.transcripts.fa` for Salmon mapping , the mapping increased from 43 % to 46.6% for one sample and from 26% to 37.7% in another sample. Other samples have ~75% mapping. Can I proceed with the differential expression now, or still ...
salmon mapping rna-seq written 1 day ago by Tania10 • updated 1 day ago by Devon Ryan73k
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Comment: C: BBMap output meaning
... Edited: Thanks genomax, much appreciated ! I will use the trimmed data and see the difference. But this also mean we have too big insert sizes at end? Does this make sense? ...
written 3 days ago by Tania10
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Comment: C: BBMap output meaning
... Sorry to bother again. But which column is the insert sizes? the count column? These are the raw data before doing anything. ...
written 3 days ago by Tania10
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Comment: C: BBMap output meaning
... I used the following command, found it somewhere in biostars: ./bbmap.sh -Xmx50g in1=Sread1.fastq.gz in2=Sread2.fastq.gz ihist=histmap1m.txt reads=1000000 ref=human_genome.fa ...
written 3 days ago by Tania10
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BBMap output meaning
... Hi All Does anyone understand the following top lines from BBMap ihist output; I use some previous biostars to run it but can't get what are the `#InsertSize` and `Count`. Does it mean the first insert size is 77? Then can we have insert sizes = 1 as in the end of the output? ...
rnaseq bbmap written 3 days ago by Tania10
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Comment: C: Salmon very low mapping
... Thanks Rob, I will try working on this. Thanks much appreciated. ...
written 3 days ago by Tania10

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