User: Santosh Anand

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Santosh Anand4.0k
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Posts by Santosh Anand

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Comment: C: Looping over plink files
... Could you write what did you try? ...
written 5 days ago by Santosh Anand4.0k
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Answer: A: how to deal with sra files which can generate three fastq files?
... Either use only the _1 and _2 files or use option `--split-files` instead of `--split-3` See the manual/help page: --split-files Dump each read into separate file.Files will receive suffix corresponding to read ...
written 7 days ago by Santosh Anand4.0k
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Comment: C: Mapping and Variant calling
... https://github.com/ekg/alignment-and-variant-calling-tutorial ...
written 8 days ago by Santosh Anand4.0k
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Comment: C: Looping over plink files
... for j in $(seq 1 22); do echo chr$j; done ...
written 8 days ago by Santosh Anand4.0k
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Comment: C: Looping over plink files
... you need another inner loop: `for j in seq 1 22` ...
written 8 days ago by Santosh Anand4.0k
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Answer: A: Samtools mpileup genotype likelihood no PL field when all individuals are 0/0
... 0/0 in all samples implies there are only REF alleles and no ALT allele is present. The PL is calculated as the probability of ALT alleles and given as a PHRED-like score (https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it). Since there are no ALT ...
written 13 days ago by Santosh Anand4.0k
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Comment: C: Replace symbols in R table
... Sorry, somehow missed your solution! *Deleting* ...
written 29 days ago by Santosh Anand4.0k
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Answer: A: Is it possible to analyze differentially expressed genes without sample replicat
... ?DESeq gives you the answer > Experiments without replicates do not allow for estimation of the > dispersion of counts around the expected value for each group, > which is critical for differential expression analysis. **The DESeq2 > authors have decided to no longer supp ...
written 4 weeks ago by Santosh Anand4.0k
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Comment: C: BLAST and LINUX
... What you need first is to understand the output of Blast. This can help : https://www.amherst.edu/system/files/media/1063/2012_Manual_11i_Drosophila_blastn.pdf ...
written 4 weeks ago by Santosh Anand4.0k
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Answer: A: Splitting genome 2bit files
... Fasta and 2bit can be easily converted back and forth https://genome.ucsc.edu/goldenpath/help/twoBit.html Chromosome-wise Fastas can be dloaded from here: http://hgdownload.cse.ucsc.edu/downloads.html#human ...
written 4 weeks ago by Santosh Anand4.0k

Latest awards to Santosh Anand

Teacher 2 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 29 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: How to import huge .csv files in R studio?
Scholar 8 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: How to import huge .csv files in R studio?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For chart title in plotly (R)
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 9 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 9 weeks ago, created an answer that has been accepted. For A: How can we download all TSA and WGS from NCBI Trace by taxon programmatically?
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Can STAR work with compressed .gz FASTQ input?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: How to recover treated/control count from DESeq2 output
Scholar 9 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to recover treated/control count from DESeq2 output
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 8 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 9 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?

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