User: Satyajeet Khare

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Satyajeet Khare1.3k
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Pune, India
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16 hours ago
Joined:
2 years, 7 months ago
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Posts by Satyajeet Khare

<prev • 270 results • page 1 of 27 • next >
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Answer: A: match gives me all NA in annotating my genes
... 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 7 months ago by Satyajeet Khare1.3k
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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 7 months ago by Satyajeet Khare1.3k
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Comment: C: Files to compare ChIP vs Input on genome browser: after alignment or peak callin
... 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 7 months ago by Satyajeet Khare1.3k
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Comment: C: Files to compare ChIP vs Input on genome browser: after alignment or peak callin
... You can use `treat_pileup.bdg.gz` for ChIP and `control_lambda.bdg.gz` file for input. ...
written 7 months ago by Satyajeet Khare1.3k
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Comment: C: Files to compare ChIP vs Input on genome browser: after alignment or peak callin
... `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 7 months ago by Satyajeet Khare1.3k
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Answer: C: Files to compare ChIP vs Input on genome browser: after alignment or peak callin
... 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 7 months ago by Satyajeet Khare1.3k
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Comment: C: Does Cufflinks report chimeric transcripts/fusion genes?
... 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 7 months ago by Satyajeet Khare1.3k
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Comment: C: samtools rmdup error
... Agreed. Except, `samtools fixmate` needs name-sorted file. Coordinate-sorted file not accepted. ...
written 7 months ago by Satyajeet Khare1.3k
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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 8 months ago by Satyajeet Khare1.3k
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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 9 months ago by Satyajeet Khare1.3k

Latest awards to Satyajeet Khare

Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Too low mapping percentage using HISAT2 on human reference genome.
Voter 6 months ago, voted more than 100 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Differentiall analysis of chip-deq data
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 9 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 10 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 12 months ago, created an answer that has been accepted. For A: error in tophat2
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Scholar 13 months ago, created an answer that has been accepted. For A: error in tophat2
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Scholar 13 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 13 months ago, created an answer that has been accepted. For A: error in tophat2
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Popular Question 15 months ago, created a question with more than 1,000 views. For fastq dump error
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 22 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 23 months ago, created an answer that has been accepted. For A: error in tophat2
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Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be

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