User: Satyajeet Khare

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Satyajeet Khare1.0k
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Pune, India
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Posts by Satyajeet Khare

<prev • 228 results • page 1 of 23 • next >
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Comment: C: Finding target genes of a TF
... 1. Look for public ChIP-Seq datasets of the TF of your interest (preferably, in the tissue of your interest) 2. Look for RNA-Seq datasets of TF-KO. Combined analysis should provide lots of clues. If the above datasets are not available, get the TF motif and check if your target genes have it ...
written 1 hour ago by Satyajeet Khare1.0k
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Comment: A: Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate a
... Your samples probably differ significantly in rRNA contamination. Do you have sorted files of rRNA reads for two samples? Do these files differ significantly in size? What is the size of kept file and discarded file for each sample? ...
written 4 hours ago by Satyajeet Khare1.0k
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Comment: C: Analyzing specific genes in a microarray (RNA expression)
... If you have done the analysis with the data and if you have not found any differentially expressed genes, there ain't much to do. You can plot expression of the set of genes (barplot, heatmap) that you are interested in but they wont show significant change as expected. I don't think you can perform ...
written 6 hours ago by Satyajeet Khare1.0k
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Answer: C: Tool for finding peaks from Chip-seq data at multiple regions.
... You can use `annotatePeaks.pl` from `HOMER`. You just need to provide the genome `fasta` file with gene `gtf` file along with the `bed` file of your ChIP-Seq peaks. ...
written 6 hours ago by Satyajeet Khare1.0k
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Comment: C: Converting a VCF with SNPs and indels to BED format
... I used the same functions in the `convert2bed` as you mentioned. It works clean. Thanks! ...
written 1 day ago by Satyajeet Khare1.0k
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Answer: C: Normalisation using Input DNA & calling peaks [Chip-seq]
... It is better that you have your own input sample. It is used as follows. macs2 -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01 where -t is Treatment or Wildtype and -c is input. ...
written 1 day ago by Satyajeet Khare1.0k
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Comment: C: Converting a VCF with SNPs and indels to BED format
... Oh yes. I am running the latest version locally (through directory). Its probably trying to access the old version which is installed globally. ...
written 1 day ago by Satyajeet Khare1.0k
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Comment: C: Converting a VCF with SNPs and indels to BED format
... Alex, I get following error with the above command. Error: Could not allocate space for VCF INFO string I have updated the `bedops` to the latest version (2.4.28) as you mentioned [here][1]. This update resolves the same error from `convert2bed` command. But the issue with `vcf2bed` remains. I ...
written 1 day ago by Satyajeet Khare1.0k
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Answer: C: Is there a way to fetch genomic sequences at given coordinates without downloadi
... [Here][1] is one way to download the sequences using DAS server. You can write a loop and fetch the sequences. [1]: https://www.biostars.org/p/56/ ...
written 1 day ago by Satyajeet Khare1.0k
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Comment: C: RNASeq lane effect
... Any particular reason you expect lane differences? I have seen technical replicates on neighbouring lanes and they look identical. ...
written 1 day ago by Satyajeet Khare1.0k

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Scholar 1 day ago, created an answer that has been accepted. For A: error in tophat2
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