User: Amitm

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Amitm1.9k
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Posts by Amitm

<prev • 240 results • page 1 of 24 • next >
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Comment: C: Stringtie duplicate transcripts
... hi, As a side-note to what has been posted already by Kristoffer, you could load the BAM and stringTie assembled GTF in your local IGV. Once there, check the [Sashimi plots][1]. If those alternate exon start/ stop sites are true, then you should see splice-junction support for both the boundaries of ...
written 4 hours ago by Amitm1.9k
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Comment: C: The number of axons in a segment
... If it is from human/ a model organism with reference annotation available, then use UCSC Table Browser or Ensembl BioMart to download exon coordinates and then use bedtools to check overlap. Alternatively, if your query segments are few, you could use the online interfaces (UCSC Table Browser) to p ...
written 6 days ago by Amitm1.9k
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Comment: C: VCF to maf
... A couple of suggestions which might be useful - 1) If you are not already using [conda][1], please do so to install vcf2maf. 2) Are you able to get VEP working? If yes, then you could run VEP with the `--pick` flag (and tabular data output) so that the output in effect is like vcf2maf. And then you ...
written 14 days ago by Amitm1.9k
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Comment: C: Suggestion needed for finding fusion transcripts
... Hi, Those are not bad lib sizes. You could surely give it a go. Though, having SE instead of paired-end reads would make it a bit more difficult for any algorithm to detect candidates. ...
written 8 weeks ago by Amitm1.9k
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Answer: C: Classifying normal vs cancer tissues from mutational data
... Hi, Is the cancer you are suspecting, a known type? If yes then it should be somewhat easier as you could check if the any of the known driver mutations have been detected. More importantly though, the mutational data that you have, is that somatic or obtained from single sample variant calling? Det ...
written 9 weeks ago by Amitm1.9k
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Answer: C: Suggestion needed for finding fusion transcripts
... Hi, I agree to prev. comment from ATpoint. Nonetheless, I have used STAR-Fusion and here are some points to keep in mind - 1. You should have good sequencing depth in your RNA-seq library to confidently detect fusions. As a rough estimate, 60M reads or more of 100x2 PE data is a good starting poin ...
written 10 weeks ago by Amitm1.9k
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Answer: C: Interested in RNA-Seq splicing analysis - go for paired-end shorter or single-en
... Hi, Assuming the sequencing template library is ~300bp (median), then a 75x2 PE data is effectively giving you information of 75 + 75 + the insert size of ~150 = ~300bp of the genome/transcriptome. Admittedly, in practice, the avg. insert size you get is mostly << 150bp as the template lib. si ...
written 10 weeks ago by Amitm1.9k
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Answer: C: How I deal with redundant genes in microarray
... Hi, Multiple probes for a given gene could indicate >1 exonic regions being targeted. To be sure, you could retrieve the genomic coordinate(s) for all the probes for such a gene and check it on a genome browser (like UCSC). Sometimes a given probe could be specific for a given transcript isoform, ...
written 10 weeks ago by Amitm1.9k
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Comment: C: Low percent of RNA-seq reads mapping
... Hi, I am not sure how much time you would want to put into finding out about the data quality. Of course the authors might be able to give you some reasons. You could also, if you haven't done already, use samtools to extract the 'secondary alignments' and manually check some of the reads using any ...
written 10 weeks ago by Amitm1.9k
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Comment: C: Low percent of RNA-seq reads mapping
... Hi, I would suggest to run [FastQC][1] on it to see if there is adapter contam., or over-represented sequences. Presence of adapter stretch in the fastq read effectively makes the 'usable' length shorter. So that is one thing to check. Also, if this is total RNA-sequencing then after rRNA depletion ...
written 11 weeks ago by Amitm1.9k

Latest awards to Amitm

Popular Question 13 days ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Scholar 8 weeks ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 10 weeks ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 10 weeks ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Appreciated 20 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Scholar 20 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 2.1 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 2.2 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 3.0 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 3.5 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 3.6 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Guru 3.6 years ago, received more than 100 upvotes.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones

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