User: Satyajeet Khare
Satyajeet Khare • 1.5k
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Posts by Satyajeet Khare
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... 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 months ago by
Satyajeet Khare • 1.5k
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4
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548
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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 5 months ago by
Satyajeet Khare • 1.5k
4
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203
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Answer:
A: problem with vcf file by gatk
... You are declaring sample name to be 20 (RGSM=20). ...
written 6 months ago by
Satyajeet Khare • 1.5k
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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 6 months ago by
Satyajeet Khare • 1.5k
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444
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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 6 months ago by
Satyajeet Khare • 1.5k
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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 7 months ago by
Satyajeet Khare • 1.5k
1
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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 7 months ago by
Satyajeet Khare • 1.5k
1
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444
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1
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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 7 months ago by
Satyajeet Khare • 1.5k
1
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1
answer
444
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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 7 months ago by
Satyajeet Khare • 1.5k
1
vote
1
answer
444
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1
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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 7 months ago by
Satyajeet Khare • 1.5k
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