User: k.kathirvel93
k.kathirvel93 • 120
- Reputation:
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Posts by k.kathirvel93
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... Hi Charles Warden,
I am happy about your reply, and now i got some idea. Can you suggest me where can i download that transcriptome FA file. I have .gtf annotation file. ...
written 5 days ago by
k.kathirvel93 • 120
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... Yes. For specific area of disease. ...
written 5 days ago by
k.kathirvel93 • 120
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... Hi EveryOne,
I am trying to benchmark RNA-seq quantification tools, While trying eXpress, i donno how to finished it up coz of reference and bam file confusion. I have aligned my paired-end RNA-seq data with Hisat2 and STAR. Can anyone suggest me a code for eXpress quantification. It ll be so helpf ...
written 5 days ago by
k.kathirvel93 • 120
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Comment:
C: RNA seq normalization(TMM)
... I suspect that you have a problem on write.csv line. Check your path is correct or not. ...
written 20 days ago by
k.kathirvel93 • 120
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Comment:
C: RNA seq normalization(TMM)
... library(edgeR)
#TMM Normalisation
lib.size <- sum(d$sample1)
scale.factors <- calcNormFactors(TMM$sample1, method = "TMM")
norm.data <- t(t(TMM$sample1)/(scale.factors*lib.size))
write.csv(norm.data,"/home/TMM.csv") ...
written 21 days ago by
k.kathirvel93 • 120
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... Hi arshad1292,
I found the way by myself, First go to normal stringtie gene abundance file and reorder the ensemblID column in alphabet order with extent selection and copy gene ID column. Second go to PrepDE.py output file gene_Count_matrix.csv, and reorder the ensemblID column in alphabet orde ...
written 24 days ago by
k.kathirvel93 • 120
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C: HISAT2 alignment Error?
... Should I do something for this warning OR i can go further ?. Because after this, i am getting more than 95 % alignment rate. Thanks ...
written 4 weeks ago by
k.kathirvel93 • 120
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Comment:
C: HISAT2 alignment Error?
... Thanks for the reply ATpoint, Here is my Adapter removal command:
cutadapt3 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o Sample_1.fastq -p Sample_2.fastq Sample1_1fastq Sample1_2.fastq
I am not getting any warning, while aligning w ...
written 4 weeks ago by
k.kathirvel93 • 120
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... Hi EveryOne,
I am working in Paired-wnd RNA-seq data set, When i am trying to align my reads against reference HG19 genome by using HISAT2, am getting this error:
Warning: skipping mate #2 of read 'ST-E00142:733:HTKKMCCXY:1:1207:16163:5229 2:N:0:ACTTGA' because it was < 2 characters long
T ...
written 4 weeks ago by
k.kathirvel93 • 120
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Answer:
A: STAR set --sjdbOverhang value
... Why don't you use sjdbOverhang 101 for your 150bp paired-end data? ...
written 5 weeks ago by
k.kathirvel93 • 120
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