User: Satyajeet Khare

gravatar for Satyajeet Khare
Satyajeet Khare1.2k
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Pune, India
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1 year, 11 months ago
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Posts by Satyajeet Khare

<prev • 262 results • page 1 of 27 • next >
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Comment: C: Bowtie2-output to file
... I don't think the double quotes will work. Can you try without them? P.S. May I know why you plan to use `--met-file`? Thanks ...
written 13 days ago by Satyajeet Khare1.2k
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HOMER Hi-C with more than one enzyme
... Biostars, I am attempting a Hi-C analysis using HOMER. I have generated a tag directory using `makeTagDirectory` command as follows. makeTagDirectory HiC-Unprocessed 3e_HiC_Rep1_1.bam,3e_HiC_Rep1_2.bam -tbp 1 Now I need to filter the TagDirectory for RE site. But my data is 3 enzyme Hi-C. I ...
hi-c homer written 5 weeks ago by Satyajeet Khare1.2k
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Comment: A: FIMO outputs only Chr1 hits
... I think `FIMO` is not able to go beyond Chr1 due to default parameters. Try playing with `--max-stored-scores` and -`-thresh` parameters. ...
written 7 weeks ago by Satyajeet Khare1.2k
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Answer: A: Setting the first row as column name in R
... Add Argument `header=TRUE` ...
written 7 weeks ago by Satyajeet Khare1.2k
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Comment: C: Expression plot of GoI using EdgeR
... Thanks a lot, @Sej and @Kevin. `Glimma` needs R to be updated. I'll just check if that wont affect my installed packages. Will try `ggplot2`. ...
written 8 weeks ago by Satyajeet Khare1.2k
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Comment: C: CuffDiff results does not seem correct
... Specific command used and percentage of mapped reads would help. ...
written 8 weeks ago by Satyajeet Khare1.2k
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Expression plot of GoI using EdgeR
... Biostars, The question is perhaps too naive, but I was wondering if there are tools to plot expression of specific gene of interest in `EdgeR`. I think there are some tools in `DESeq` such as `plotCounts`, but I could not find parallel in `EdgeR`. Is there any? Best, ...
rna-seq written 8 weeks ago by Satyajeet Khare1.2k • updated 8 weeks ago by Kevin Blighe12k
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Comment: C: MEME-FIMO return different count of target for the same sequence
... I think your background model will be different for whole genome and its fragments. And that might be the reason for the differences in motif detection. ...
written 10 weeks ago by Satyajeet Khare1.2k
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Comment: C: Research Bazaar 2018
... Vijay, would you please message me if you hear anything from the organisers? Thanks! ...
written 10 weeks ago by Satyajeet Khare1.2k
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Comment: C: hisat2-build indexing produces more than 8 output files
... Yup. So my guess is that your indexing may have stopped due to RAM issues. You can still provide the 'splice sites' file at the time of alignment. Best ...
written 10 weeks ago by Satyajeet Khare1.2k

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