User: hafiz.talhamalik
hafiz.talhamalik • 110
- Reputation:
- 110
- Status:
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- Location:
- Pakistan
- Twitter:
- @hafizmuhdtalha
- Last seen:
- 1 day, 9 hours ago
- Joined:
- 3 years, 10 months ago
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Posts by hafiz.talhamalik
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... try R package CoRegNet
[1]https://bioconductor.org/packages/release/bioc/html/CoRegNet.html
[Metascape] [1]: http://metascape.org/gp/index.html#/main/step1 ...
written 23 days ago by
hafiz.talhamalik • 110
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Comment:
C: Help with data from rna-seq
... you should elaborate your question. it's not clear.
also as mentioned by @h.mon looks like you are mixing transcriptome and genome analysis ...
written 7 weeks ago by
hafiz.talhamalik • 110
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C: Problem in featureCounts file.
... Yeah Thanks. got it. ...
written 7 weeks ago by
hafiz.talhamalik • 110
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C: Problem in featureCounts file.
... looks like multiple location of same gene ...
written 7 weeks ago by
hafiz.talhamalik • 110
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... I am using featureCounts for my RNA-seq data to get count matrix. but m facing some problem with my output file.
Most of the file is fine but there are few lines which shows multiple chromosome number and length etc parameters so file becomes quite weired.
few lines of Output file as follows
L ...
written 7 weeks ago by
hafiz.talhamalik • 110
• updated
7 weeks ago by
genomax ♦ 71k
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... yes i want common DE genes. Thanks for the answer. ...
written 10 weeks ago by
hafiz.talhamalik • 110
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... That could be the one solution to do like this. but we have anova test for multiple sample testing. I m more interested in that if we could apply that for rna-seq analysis..
let me check DMRseq package as well. ...
written 10 weeks ago by
hafiz.talhamalik • 110
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5 follow
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... How can i perform differential gene expression for 3 groups sample ? edgeR uses t-test which can be used for 2 groups. So how can I do it for 3 groups ?
my experiment design is like
Normal vs disease condition 1 vs disease condition 2 ...
written 10 weeks ago by
hafiz.talhamalik • 110
• updated
10 weeks ago by
ATpoint ♦ 23k
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... One more thing. GATK 4 doesn't have the option of TargetRealignmentCreator, so what's the alternate of it ? do we apply haplotype caller directly on marked-duplicate.bam file ? ...
written 3 months ago by
hafiz.talhamalik • 110
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... ok. let me try with this ...
written 3 months ago by
hafiz.talhamalik • 110
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For Threshold of removing genes with low counts ?
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For Which package to use for RPKM/FPKM RNA-seq counts?
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