User: Bioinfosm

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Bioinfosm620
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Translational research using next-gen sequencing (#NGS), #bioinformatics, #genomics and loads of #bigData digesting... @MSKCC

Posts by Bioinfosm

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Method To Identify Viral Integration Site In Human Genome From Ngs Data?
... Any update on this in 2017 .. what has been the experience and any new ones worth trying? Especially for viral integration detection from DNA capture based NGS data. thanks! ...
written 23 months ago by Bioinfosm620
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Comment: C: RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
... Guess that is a tough question. I would say that the tools wouldnt really go head to head on which one is better. But the real questions is 'what type of QC' is someone looking for. And this depends on the research question being asked from the RNA-seq data. The common tools would do some things si ...
written 4.3 years ago by Bioinfosm620
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Comment: C: Plot Coverage Vs. Gc Content
... This was very helpful, thanks for the discussion and sharing.   You do mention 'handful of regions' but I cant figure in the code where those select regions are used for the plot. In other words, assuming exome or targeted sequencing data, one would like to use a substring of the chrZ in order to ...
written 4.4 years ago by Bioinfosm620
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Comment: C: Do read pairs matter in alignment?
... Sure, or even better. If you are not sure what aligner was originally used or have a better one to try! You can use something like samtools flagstat and compare how your aligned BAM file is same/better than the original one. ...
written 4.6 years ago by Bioinfosm620
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Answer: A: Do read pairs matter in alignment?
... The steps sound fine, and as others have suggested, using both read1 and read2 for alignment is more efficient. The paired mapping allows for better read placement, especially over repetitive or homologous regions. Am not sure why you dont directly use the aligned BAM file to call variants on chr12 ...
written 4.6 years ago by Bioinfosm620
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Comment: C: Amino Acid Change To Genomic Location
... The uniprot ID Q9P2D8 supposedly maps to this ENSP which seems incorrect! In fact, it should have been ENSP00000376858, which works out fine with VEP as well. Am checking with the Uniprot team on that. Thanks once again! ...
written 6.1 years ago by Bioinfosm620
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Comment: C: Amino Acid Change To Genomic Location
... Emily, thanks for pointing that! I was able to format my data to HGVS and use VEP to obtain coordinate and codon. However, some do not get any output via VEP!! ENSP00000256339:p.Val1597Ala returns a blank in VEP. Though it works just fine in polyphen2! http://genetics.bwh.harvard.edu/ggi/pph2/3a7d3e ...
written 6.1 years ago by Bioinfosm620
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Comment: C: Amino Acid Change To Genomic Location
... I like the idea of being able to use ensembl, but is there any way to get the nucleotide as well! My example variant was: VAR_031436 Q9NXK6 MPRG_HUMAN p.Ile24Thr Which I need nucleotide and chromosome-coordinate for, and this is the corresponding link which gives me chr-location, ...
written 6.1 years ago by Bioinfosm620
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Comment: C: Get A Graphical Representation Of Number Of Reads In Bam File For A Certain Geno
... is this faster than samtools mpileup? That command gives depth at each position along with some additional information ...
written 6.6 years ago by Bioinfosm620
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Comment: C: Does It Makes Sense To Assemble All My Rna-Seq Samples As Though They Were One?
... Unless it is the same sample, you might be better off to run independent tophat analysis to find all the transcripts separately. Then there is always the option of combining all those to form the inclusive 'transcriptome' ...
written 6.6 years ago by Bioinfosm620

Latest awards to Bioinfosm

Appreciated 4.3 years ago, created a post with more than 5 votes. For Resources For Video/Webcasts Of Talks/Seminars/Courses
Epic Question 4.3 years ago, created a question with more than 10,000 views. For Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elements
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Resources For Video/Webcasts Of Talks/Seminars/Courses
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Plos Paper - Rise And Demise Of Bioinformatics... Overly Negative Undertones
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Tophat Gene Models Merging
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elements
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Scholar 4.3 years ago, created an answer that has been accepted. For A: Do read pairs matter in alignment?
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Calling Genotypes On Multiple Trios
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Great Question 4.6 years ago, created a question with more than 5,000 views. For Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elements
Scholar 4.6 years ago, created an answer that has been accepted. For A: Do read pairs matter in alignment?
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Teacher 7.4 years ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
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