User: Santosh Anand

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Santosh Anand1.5k
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Posts by Santosh Anand

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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... Pastr some lines in the main Q, where annovar is missing the annotation. Or better, upload part of the file to somewhere and attach a link here ...
written 16 hours ago by Santosh Anand1.5k
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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... I'm not sure annovar if looks at the sample annotation. AFAIR it derives the concordance by looking at chrom post ref and alt only ...
written 16 hours ago by Santosh Anand1.5k
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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... What do you mean by monomorphic? If there is an rsID, it should correspond to at least a SNP ...
written 16 hours ago by Santosh Anand1.5k
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Answer: A: Error building database in snpEff
... The path to genome might be wrong. See http://snpeff.sourceforge.net/SnpEff_manual.html#buildGtf Note: The FASTA file can be either in /path/to/snpEff/data/genomes/mm37.61.fa or in /path/to/snpEff/data/mm37.61/sequences.fa ...
written 1 day ago by Santosh Anand1.5k
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Comment: C: High correlation between two genes or more genes indicative of similar localizat
... I would not be very confident to say anything < 0.8 a high correlation. ...
written 1 day ago by Santosh Anand1.5k
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Comment: C: Is samtools' compression of bam to cram lossless?
... My guess is that it will be 'lossless'. If it were lossy, it must have been documented. You can easily check it by yourself. Get a sam -> convert to bam -> cram -> sam. Then compare this sam with original sam. ...
written 3 days ago by Santosh Anand1.5k
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Answer: A: How to recover treated/control count from DESeq2 output
... # Un-normalized counts counts(deseq) # Normalized counts (Normalized for size factors) counts(deseq, normalized = TRUE) Be aware that the log2FoldChance reported by DESeq2 is shrunk. So it will be usually lesser than what calculated from your normalized counts data. See the DE ...
written 4 days ago by Santosh Anand1.5k
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Comment: C: Small RNA-seq experimental design, which one is better?
... Your may like to add "pooling" in title and keyword of the Q. ...
written 4 days ago by Santosh Anand1.5k
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Answer: A: Small RNA-seq experimental design, which one is better?
... We have some experience in pooling for DNA-sequencing, and it worked quite well for variant call and allele frequency estimation (using a pool size of 12) https://www.nature.com/articles/srep33735 This review paper discusses many aspects of pooling in DNA-sequencing https://www.nature.com/nrg/jour ...
written 4 days ago by Santosh Anand1.5k
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Comment: C: Rsubread/subread installation on Windows
... What have you tried and what's the error message you get? Did the Cygwin install correctly? On a side note: move to Linux (even inside a virtual machine on windows), it will save you a lot of future pains given that you are doing bioinformatics. ...
written 5 days ago by Santosh Anand1.5k

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Teacher 3 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
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Scholar 13 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
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