User: Amitm

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Amitm1.5k
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Posts by Amitm

<prev • 201 results • page 1 of 21 • next >
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Comment: C: How to find Novel transcripts
... Have you seen here ? https://www.nature.com/articles/nbt.1883 There are other tools like [Trinity][1], but its documentation is good and there are lots of downstream tools to play around with the assembled fasta. [1]: https://github.com/trinityrnaseq/trinityrnaseq/wiki ...
written 3 months ago by Amitm1.5k
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Comment: C: StringTie inconsistent expression value
... Have you loaded the BAM into IGV and gone into that locus to check? Most of the times, inspecting in IGV resolves doubt about differences in expression estimate (from assembler). ...
written 3 months ago by Amitm1.5k
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Comment: C: STAR do i need --twopassMode ?
... Hi, I am not sure what would be the full effect on the BAM due to the param. Besides, I have not used rMATS myself. So I don't have anything specific to comment. Time permitting, you can run one sample w and w/o that param and check the alignment% and the count data. I haven't come across the need t ...
written 3 months ago by Amitm1.5k
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Comment: C: STAR do i need --twopassMode ?
... Hi again, Are you looking for chimera discovery? Then I would recommend that you could follow the guidelines of STAR-Fusion tool. On this page [here][1], are the params that enables more sensitivity for chimera detection. If you just want to increase sensitivity to splice-detection, then on `page 7 ...
written 3 months ago by Amitm1.5k
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Answer: C: STAR do i need --twopassMode ?
... Hi, Though I haven't done a comparative analysis of using & not-using that param, but it definitely helps if you are interested in splicing analysis. Specially if you are going to do transcriptome assembly (using Cufflinks or StringTie like tools). I analyzed CRISPR treated samples and I was abl ...
written 3 months ago by Amitm1.5k
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Comment: C: Help exploring unknown region
... Jean-Karim's answer below reminded me of this browser where you can explore effect of chromatin interaction [3D genome browser][1] especially relevant in topologically associate domains (TADs)/ CTCF binding sites [1]: http://promoter.bx.psu.edu/hi-c/ ...
written 3 months ago by Amitm1.5k
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Comment: C: Help exploring unknown region
... Hi, Some suggestions. you might have checked already - 1) On [UCSC Genome Browser][1], turn on the ENCODE region regulatory and expression level tracks. Though from cell line, there is a range of cell lines and stem cells and different histone marks & concurrent expression levels. 2) Recently, F ...
written 3 months ago by Amitm1.5k
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Comment: C: gene expression database for quary a gene
... In addition to HPRD and cBioPortal, there is [CCLE][1] as well which is cell line specific Though cBioPortal has added advantage of being able to visualize effect of mut. vs. WT on the gene which you have queried. [1]: https://portals.broadinstitute.org/ccle ...
written 3 months ago by Amitm1.5k
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Comment: C: How do I normalize this data for plotting?
... Hi, I suppose the reads are assumed to be coming from a reference genome/ transcriptome. In that case, normalizing by mapping % might be one way. So instead of counts of A/C/T/G, you could have proportion of A/C/T/G in mapped reads vs. unmapped reads. So, if the base composition is changing, lookin ...
written 4 months ago by Amitm1.5k
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Comment: C: VCF format tool question
... Hi, A general remark, not sure if it would be useful. Is this targeted/ amplicon sequencing data? I have observed many a times higher noise in such data. I then remove reads which do not have both pairs mapped and also those with pairs on different chr. Sometimes pseudogenes would lead to cross-mapp ...
written 4 months ago by Amitm1.5k

Latest awards to Amitm

Scholar 3 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 5 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 10 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 11 months ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 14 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 21 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 21 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
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Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
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