User: Satyajeet Khare
Satyajeet Khare • 1.2k
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Posts by Satyajeet Khare
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... For Affy ST arrays, you can use `oligo` `read.celfiles` function like this...
> rawData <- read.celfiles(celFiles)
You can try normalization
> Data <- rma(rawData)
And finally try annotation on normalized data
> Data <- annotateEset(Data, hugene10sttranscriptcluster.db)
You m ...
written 9 weeks ago by
Satyajeet Khare • 1.2k
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Comment:
C: CRAM vs BAM
... Partly covered [here][1]. Actually CRAM is recommended for long term storage. See [here][2].
[1]: https://www.biostars.org/p/106047/
[2]: https://www.uppmax.uu.se/support/user-guides/using-cram-to-compress-bam-files/ ...
written 11 weeks ago by
Satyajeet Khare • 1.2k
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286
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... You can show reads only from `treat_pileup.bdg.gz` file for regions where you observe significant peak. The peak is called at a region because no significant reads were observed in Input sample in that locus. ...
written 11 weeks ago by
Satyajeet Khare • 1.2k
1
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286
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... You can use `treat_pileup.bdg.gz` for ChIP and `control_lambda.bdg.gz` file for input. ...
written 11 weeks ago by
Satyajeet Khare • 1.2k
0
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2
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286
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... `peak.bed` file tells you which peaks are "real". There is only one `peaks.bed` file and it contains the co-ordinates of the statistically significant peaks. ...
written 11 weeks ago by
Satyajeet Khare • 1.2k
1
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286
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... You can use `treat_pileup.bdg.gz` files and `peaks.bed` file. Bam files are not normalized to sequencing depth and are bigger in size. ...
written 11 weeks ago by
Satyajeet Khare • 1.2k
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167
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... According to [this][1] link, yes. But aligner such as `Tophat-fusion`, should provide you the results directly for validation. [This][2] is an example in the `Tophat-fusion` manual. Don't know about other aligners.
[1]: http://www.egr.msu.edu/changroup/Protocols/NGS%20analysis%20example%20of%20a ...
written 12 weeks ago by
Satyajeet Khare • 1.2k
0
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1
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431
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1
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Comment:
C: samtools rmdup error
... Agreed. Except, `samtools fixmate` needs name-sorted file. Coordinate-sorted file not accepted. ...
written 12 weeks ago by
Satyajeet Khare • 1.2k
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2.8k
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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 3 months ago by
Satyajeet Khare • 1.2k
0
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233
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... 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 ...
written 4 months ago by
Satyajeet Khare • 1.2k
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7 weeks ago,
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9 weeks ago,
created a question with more than 1,000 views.
For Replace XLOC id with gene symbol in FPKMmatrix function
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For A: Differentiall analysis of chip-deq data
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