User: Satyajeet Khare

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Satyajeet Khare1.3k
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Pune, India
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13 hours ago
Joined:
2 years, 8 months ago
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Posts by Satyajeet Khare

<prev • 272 results • page 1 of 28 • next >
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Comment: C: Reference allele is too long message GATK
... 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 Khare1.3k
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Comment: C: Convert colorspace fastq to basespace fastq
... 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 Khare1.3k
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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 9 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 9 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 9 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 9 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 9 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 9 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 9 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 9 months ago by Satyajeet Khare1.3k

Latest awards to Satyajeet Khare

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Too low mapping percentage using HISAT2 on human reference genome.
Voter 8 months ago, voted more than 100 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Differentiall analysis of chip-deq data
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 11 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 11 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 11 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 11 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 14 months ago, created an answer that has been accepted. For A: error in tophat2
Guru 14 months ago, received more than 100 upvotes.
Scholar 14 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 14 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 14 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 15 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 16 months ago, created an answer that has been accepted. For A: error in tophat2
Popular Question 17 months ago, created a question with more than 1,000 views. For fastq dump error
Teacher 23 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 24 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 2.1 years ago, created an answer that has been accepted. For A: error in tophat2
Teacher 2.1 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
Scholar 2.2 years ago, created an answer that has been accepted. For A: error in tophat2

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