User: Satyajeet Khare

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Satyajeet Khare1.5k
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Posts by Satyajeet Khare

<prev • 290 results • page 1 of 29 • next >
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Answer: C: Converting multiple GSE data into expression matrix
... 1. Create a Gene level expression matrix by combining probe IDs. 2. Remove batch effect (e.g. using limma). 3. Use for WGCNA ...
written 5 weeks ago by Satyajeet Khare1.5k
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Comment: C: edgeR gives no DE genes <0.05 FDR
... Incomplete information. Can you provide the complete script? How do the samples look on PCA plot or distance matrix? ...
written 8 weeks ago by Satyajeet Khare1.5k
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Answer: A: problem with vcf file by gatk
... You are declaring sample name to be 20 (RGSM=20). ...
written 10 weeks ago by Satyajeet Khare1.5k
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Comment: C: HISAT2 index building
... Index with --ss and --exon options on large genomes (e.g. human, mouse, zebrafish etc.) only if you have more than 200 GB RAM. If not index simply like this hisat2-build -p 10 genome.fa genome You can provide the exon information at the time of alignment like this hisat2 --known-splicesit ...
written 11 weeks ago by Satyajeet Khare1.5k
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Comment: C: DE novo call from trio
... Sorry about the late reply. Did you get an error without "convert to biallelic" step this time too? ...
written 12 weeks ago by Satyajeet Khare1.5k
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Comment: C: DE novo call from trio
... The link did not open, but assuming that you have a vcf file from the same source and corresponding to the same genome version you used for alignment, it should work. But I would still recommend using GATK bundle since you may need some files in future which are exclusively present in the GATK bundl ...
written 3 months ago by Satyajeet Khare1.5k
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Comment: C: DE novo call from trio
... Yes, you need to perform the alignment again. I think it will affect the outcome because the coordinates of the vcf file won't match the alignment files in current scenario. ...
written 3 months ago by Satyajeet Khare1.5k
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Comment: C: DE novo call from trio
... Oh, its select biallelic. Anyway, as I mentioned, I never had to do this step. Regarding the last point (and this may get rid of this biallelic issue), you need to use b37 package for all files. Assuming you downloaded the vcf file `1000G_phase1.snps.high_confidence.b37.vcf.gz` from [this link][1] ...
written 3 months ago by Satyajeet Khare1.5k
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Comment: C: DE novo call from trio
... No, gvcf wont change the results. Just that adding samples later will be easier. I am not sure why "convert to biallelic" step is necessary. I also worked only on SNPs but did not run this command. Everything else looks fine. What were the hard filtration parameters? Important: You may want to use ...
written 3 months ago by Satyajeet Khare1.5k
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Comment: C: DE novo call from trio
... Its possible. But I think following change would help. 1. After BQSR, create g.vcf files for each sample using `HaplotypeCaller` `-ERC GVCF` option. 2. Create a combined genotype using `GenotypeGVCFs` 3. Separate SNPs and Indels using `SelectVariants` and perform hard filtration 4. Comb ...
written 3 months ago by Satyajeet Khare1.5k

Latest awards to Satyajeet Khare

Popular Question 19 days ago, created a question with more than 1,000 views. For SpliceR genome session error
Scholar 5 weeks ago, created an answer that has been accepted. For A: error in tophat2
Teacher 10 weeks 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
Popular Question 3 months ago, created a question with more than 1,000 views. For Differential expression analysis with RNA-Seq samples that vary in depth
Teacher 6 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
Teacher 7 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
Popular Question 10 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 10 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 13 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Too low mapping percentage using HISAT2 on human reference genome.
Voter 20 months ago, voted more than 100 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Differentiall analysis of chip-deq data
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Scholar 24 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 24 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
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Scholar 2.2 years ago, created an answer that has been accepted. For A: error in tophat2
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Scholar 2.2 years ago, created an answer that has been accepted. For A: error in tophat2
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