User: gundalav
gundalav • 230
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Posts by gundalav
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... @ATPoint Thanks for your reply. Speed is less of a concern at the moment, but rather the **correctness** of Method1. I tried using `cut -f1,2,6,7,8,9`. But the Method1 is totally uncorrelated (different) from Method2 and Method3. I need to be convinced why Method1 is incorrect. Your enlightenment wi ...
written 18 days ago by
gundalav • 230
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... I have the following BAM file and a annotation file.
The BAM is a paired end alignment.
What I want to do is to calculate reads (as fragment) count in
I can do it with the following three methods.
- **Method1:** [bedtools intersect][1]
- **Method2:** [bedtools multicov][2]
- **Method3:** [fea ...
written 18 days ago by
gundalav • 230
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... Thanks. `airway@assays$data$counts` is that normalized or not? If not how can I get the normalized one from S4? ...
written 5 months ago by
gundalav • 230
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... I have the following DESeq2 code and the corresponding results
suppressMessages(library(DESeq2))
suppressMessages(library(airway))
data(airway)
airway_se <- airway
airway_dds <- DESeqDataSet(airway_se, design = ~cell + dex)
deseq <- DESeq(airway_dds)
#> ...
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... @b.nota i.e. 100 + 30 = 130 (sum of 7th column of featureCounts output)?? ...
written 6 months ago by
gundalav • 230
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... @b.nota in other words the `totalReads` in the calculation *is not the total assigned reads to the genes*? So I have to directly count from the BAM file? Would prefer to recode cause later need to calculate TPM as well. ...
written 6 months ago by
gundalav • 230
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... I'm interested in processing from featureCounts not htseq. ...
written 6 months ago by
gundalav • 230
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... Lets say the [featureCounts][1] output is this (for convenience only contain 2 genes:
Geneid Chr Start End Strand Length myfile.bam
Xkr4 chr1;chr1;chr1 3214482;3421702;3670552 3216968;3421901;3671498 -;-;- 3634 100
Npbwr1 chr1 5913707 5917398 - 3692 30 ...
written 6 months ago by
gundalav • 230
• updated
6 months ago by
James Ashmore • 2.0k
2
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... In my Amazon EC2 instance I have the following:
ubuntu@ip-333-31-16-230:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 79G 0 79G 0% /dev
tmpfs 16G 8.8M 16G 1% /run
/dev/xvda1 985G 136G 809G 15% /
tmpfs ...
written 7 months ago by
gundalav • 230
• updated
7 months ago by
Devon Ryan ♦ 70k
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... Hi Devon,
Thanks for the reply:
Do you mean this command?
trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 --paired -a CTGTCTCTTATA -a2 CTGTCTCTTATA -o $TRIMGALORE_DIR $READ1 $READ2
...
written 7 months ago by
gundalav • 230
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