User: Satyajeet Khare
Satyajeet Khare • 1.3k
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Posts by Satyajeet Khare
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... This worked fine for me.
java -jar GenomeAnalysisTK.jar -T ValidateVariants --reference_window_stop >= 300 -R Genome.fa --variant:VCF All.vcf.gz ...
written 8 days ago by
Satyajeet Khare • 1.3k
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... Assuming that the data you need is not available on any other platform, you may want to use colorspace reads directly for the analysis. No need to convert the reads. You can use Tophat with bowtie1 option. Use bowtie version 0.12.7 or lower. ...
written 7 weeks ago by
Satyajeet Khare • 1.3k
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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 months ago by
Satyajeet Khare • 1.3k
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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 9 months ago by
Satyajeet Khare • 1.3k
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602
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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 9 months ago by
Satyajeet Khare • 1.3k
1
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602
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... You can use `treat_pileup.bdg.gz` for ChIP and `control_lambda.bdg.gz` file for input. ...
written 9 months ago by
Satyajeet Khare • 1.3k
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2
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602
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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 9 months ago by
Satyajeet Khare • 1.3k
1
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2
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602
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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 9 months ago by
Satyajeet Khare • 1.3k
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336
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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 9 months ago by
Satyajeet Khare • 1.3k
0
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1
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900
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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 9 months ago by
Satyajeet Khare • 1.3k
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