User: rohitsatyam102

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Posts by rohitsatyam102

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Comment: C: DEXSeq aggregates two different genes together
... @rowan-taylor1 please give a thumbs up if it solved your problem. ...
written 9 hours ago by rohitsatyam102110
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Comment: C: DEXSeq aggregates two different genes together
... Check if you by mistake copied the bin numbers present after the **":"** something like this:- ENSG00000157315.5+ENSG00000213380.15:E001 remove :E001 or if you forgot to put like .15 present in one of my ensemble IDs. I would like to see the list of IDS you are using because small prob ...
written 2 days ago by rohitsatyam102110
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Comment: C: hg38 Ig regions
... Hi emmanouil.a. Can you help me how to do that for hg19? ...
written 4 days ago by rohitsatyam102110
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Thanks Kevin for providing clarity. ...
written 5 days ago by rohitsatyam102110
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Sure.Will remember. Thanks!! ...
written 5 days ago by rohitsatyam102110
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Comment: C: Strange MA plot from DESeq2
... This worked for me too ...
written 5 days ago by rohitsatyam102110
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Hi Kevin, in regards to the option `blind=FALSE` I wish to know what effect will it have if turned true. I was attending RNASeq course on datacamp which recommends to turn it to true to make the vst/rlog blind to the information provided in sampleTable for QC purposes. Is there a very tempting reas ...
written 5 days ago by rohitsatyam102110
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(Closed) ExpressionNormalizationWorkflow R package throws error
... Hi Everyone!! I am using the [following][1] package for SVA analysis. Using normalized log2 values from DESeq2 object. However, I am getting the error at the SVA step. The entire code is as follows: sampleTable <- read.csv("samplesheet.csv", header = T, stringsAsFactors = FALSE, sep = ",") ...
normalisation rna-seq sequencing written 5 days ago by rohitsatyam102110
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Answer: C: DEXSeq aggregates two different genes together
... Hi Kevin. First of all, thanks for responding. I did the analysis and realized that the -r option is throwing 1/4th of my reads into the "empty" category which I think is not considered while performing Differential Exon Usage. I have raised a question [here][1] regarding the same. However, not usin ...
written 5 days ago by rohitsatyam102110
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Comment: C: DEXSeq gives most of the reads as "_empty"
... Alignments were performed using RSEM, GRCh38, v33 primary assembly, STAR aligner. I used the following command bsub -e rsem.e -o rsem.o -n 32 -q regularq rsem-calculate-expression --star-output-genome-bam --strandedness reverse -p 32 --calc-pme --calc-ci --keep-intermediate-files --append-name ...
written 9 days ago by rohitsatyam102110

Latest awards to rohitsatyam102

Scholar 6 hours ago, created an answer that has been accepted. For C: Sorting the BEd File
Appreciated 7 weeks ago, created a post with more than 5 votes. For What are chromatin states ?
Scholar 5 months ago, created an answer that has been accepted. For C: Sorting the BEd File
Supporter 7 months ago, voted at least 25 times.

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