User: Satyajeet Khare

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Satyajeet Khare1.5k
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Posts by Satyajeet Khare

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Answer: A: Concatenating fastq.gz files across lanes
... cat *S1*R1* >> S1_R1.fastq.gz Where S1 is sample name in sample sheet. This can also be done folder="/Your_directory"; for value in $(cat ${folder}/sample_sheet.csv | tail -n +24 | tr -s ' ' | cut -d, -f1); do cat ${folder}/Output/*S${value}*R1* >> ${folder}/Output/S${value} ...
written 13 days ago by Satyajeet Khare1.5k
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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 9 months 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 10 months 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 months 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 10 months 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 10 months 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 11 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 11 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 11 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 11 months ago by Satyajeet Khare1.5k

Latest awards to Satyajeet Khare

Popular Question 3 months ago, created a question with more than 1,000 views. For SpliceR genome session error
Great Question 5 months ago, created a question with more than 5,000 views. For fastq dump error
Popular Question 8 months ago, created a question with more than 1,000 views. For SpliceR genome session error
Scholar 9 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
Popular Question 11 months ago, created a question with more than 1,000 views. For Differential expression analysis with RNA-Seq samples that vary in depth
Teacher 13 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 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
Popular Question 18 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 18 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 21 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Too low mapping percentage using HISAT2 on human reference genome.
Voter 2.4 years ago, voted more than 100 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Differentiall analysis of chip-deq data
Teacher 2.5 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 2.6 years ago, created an answer that has been accepted. For A: error in tophat2
Teacher 2.6 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 2.6 years ago, created an answer that has been accepted. For A: error in tophat2
Teacher 2.6 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 2.8 years ago, created an answer that has been accepted. For A: error in tophat2
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Scholar 2.9 years ago, created an answer that has been accepted. For A: error in tophat2
Teacher 2.9 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 2.9 years ago, created an answer that has been accepted. For A: error in tophat2

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