User: gundalav

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gundalav210
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Posts by gundalav

<prev • 43 results • page 1 of 5 • next >
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Comment: C: How to recover treated/control count from DESeq2 output
... Thanks. `airway@assays$data$counts` is that normalized or not? If not how can I get the normalized one from S4? ...
written 3 days ago by gundalav210
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How to recover treated/control count from DESeq2 output
... 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) #> ...
rna-seq dseq2 written 4 days ago by gundalav210 • updated 4 days ago by b.nota2.9k
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Comment: C: How to calculate RPKM from featureCounts output
... @b.nota i.e. 100 + 30 = 130 (sum of 7th column of featureCounts output)?? ...
written 8 weeks ago by gundalav210
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Comment: C: How to calculate RPKM from featureCounts output
... @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 8 weeks ago by gundalav210
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Comment: C: How to calculate RPKM from featureCounts output
... I'm interested in processing from featureCounts not htseq. ...
written 8 weeks ago by gundalav210
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How to calculate RPKM from featureCounts output
... 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 ...
rna-seq written 8 weeks ago by gundalav210 • updated 8 weeks ago by James Ashmore1.5k
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Problem Converting BAM to SAM on to Amazon-S3 Using Samtools
... 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 ...
samtools amazon-web-services amazon-ec2 amazon-s3 written 9 weeks ago by gundalav210 • updated 9 weeks ago by Devon Ryan64k
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Comment: C: TrimGalore parameter form Nextera paired-end reads adapter removal
... 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 10 weeks ago by gundalav210
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TrimGalore parameter form Nextera paired-end reads adapter removal
... I have Nextera data, according to the **[document][1]**, the adapter is this: ![enter image description here][2] My question is what's the right parameter to use for trim_galore? Does this command suffice? trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 --paired --nextera - ...
illumina adapter nextera trimming sequencing written 10 weeks ago by gundalav210 • updated 10 weeks ago by Devon Ryan64k
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Comment: C: Why mapping rate is low after adapter trimming paired-end data?
... I tried with your suggestion, doesn't change: ` trim_galore --stringency 5 --dont_gzip --paired --trim1 --length 30 -q 0 -a CTGTCTCTTATACACATCT -o $TRIMGALORE_DIR $READ1 $READ2 ` ...
written 10 weeks ago by gundalav210

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