User: Santosh Anand

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Santosh Anand2.3k
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Posts by Santosh Anand

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Answer: A: Enrichr analysis using ranked gene list
... Did you see their publication? https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377 > **Computing enrichment** > Enrichr implements three approaches to compute > enrichment. The first one is a standard method implemented within most > enrichment analysis tools: the Fishe ...
written 9 days ago by Santosh Anand2.3k
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Answer: A: What happens during seed stitching when STAR initially gets the wrong MMP?
... > "Given a read sequence R, read location i and a reference genome > sequence G, the MMP(R,i,G) is defined as the longest substring (Ri, > Ri+ 1, … , Ri+MML− 1) that matches exactly one or more substrings of > G" If I understood correctly, the MMP is for per genome. So STAR should get d ...
written 19 days ago by Santosh Anand2.3k
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Comment: C: FTP for cDNAs\mRNAs
... some hints: you can use `wget`. It supports ftp and with `-f` option, you can read the URLs from a local file. ...
written 23 days ago by Santosh Anand2.3k
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Answer: A: STAR genomeLoad overlap conflict
... My guess is that you are somehow starting the STAR job before `genomeLoad LoadAndExit` has finished loading the genome. Try with these: 1) Don't use `genomeLoad LoadAndExit`, as this is not necessary if you use `genomeLoad LoadAndKeep` later 2) use only `genomeLoad LoadAndKeep` 3) Run `genomeLoad ...
written 24 days ago by Santosh Anand2.3k
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Comment: C: fastqc: kmer-content failed
... Did you check the other read pair why it not mapping? May be this is adaptor contamination, may be low quality. And one of your problems is the `--very-sensitive-local` mode, which will bias bowtie2 to look for local instead of end-to-end match. Try running with default params. ...
written 4 weeks ago by Santosh Anand2.3k
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Comment: C: get variables in two separate lines
... And what's the problem with option A? why you need to keep all the data of a file inside a variable ?! PS: And I'll tell you, don't play with the white-space characters inside a variable; you are definitely going to burn and it hurts. PPS: This is happening because the bash shell splits the words ...
written 5 weeks ago by Santosh Anand2.3k
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Answer: A: get build 37 positions from dbSNP rsIDs
... One of the easiest ways is to use dbSNP database pre-formatted in annovar format from here (v147) http://www.openbioinformatics.org/annovar/download/hg19_avsnp147.txt.gz It looks like this: 1 10019 10020 TA T rs775809821 1 10020 10020 A - rs775809 ...
written 5 weeks ago by Santosh Anand2.3k
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... You might have fusion genes, like [Philadelphia Chromosome][1]. Normally, an aligner will align wherever it finds the best match. The best match will be decided by some sort of final score, the calculation of which could be tuned according to the experimental need by changing the parameters of alig ...
written 5 weeks ago by Santosh Anand2.3k
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Comment: C: EOF marker is absent
... Can you paste the verbatim error message here? ...
written 5 weeks ago by Santosh Anand2.3k
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Comment: C: picard MarkDuplicates find EOF problem
... **EOF may or may not be present**, *but it was not expected in either case* (means that the bam file was end prematurely, owing to some corruption) ...
written 5 weeks ago by Santosh Anand2.3k

Latest awards to Santosh Anand

Scholar 4 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 11 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Voter 24 days ago, voted more than 100 times.
Scholar 5 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: read.table does not read in all rows!
Scholar 6 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 7 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
Scholar 8 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 9 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 10 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 10 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot

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