User: alex.rubinsteyn

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Posts by alex.rubinsteyn

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Kmer Content in FastQC failed
... I have the same problem, also with 125bp paired end Illumina sequencing. The issue appears to be a shorter than desired fragment size distribution leading to adapter read-through on ~10k reads. ...
written 2.7 years ago by alex.rubinsteyn130
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Answer: A: How To Get The 3' Utr Given Geneid And Transcriptid In Ensembl Using Python?
... A possibly more convenient solution: https://github.com/hammerlab/pyensembl ...
written 3.3 years ago by alex.rubinsteyn130
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Comment: C: Best local aligner for finding fusion events?
... I would expect any tool which is actually meant for this kind of task to perfectly map a synthetic dataset with 20bp overlap at the insertion site. Even once you move into real data (with sequencing errors & variable degrees of overlap) an 8% rate of unmapped reads seems like a lot. ...
written 4.1 years ago by alex.rubinsteyn130
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Annotating a variant's effect: frameshift or nonsense?
... I'm looking at a mutation which, due to a frameshift, immediately introduces a stop codon. When describing the effect of this mutation would you call it a "frameshift", a "nonsense" mutation, or some hybrid of the two?   More broadly, I'm trying to figure out the right terminology for talking abou ...
variant effect annotation written 4.4 years ago by alex.rubinsteyn130 • updated 4.4 years ago by Pierre Lindenbaum120k
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Appropriate number of reads for assembling novel transcripts with Trinity?
... I'd like to detect novel transcripts in a cancer sample with Trinity. I'm sequencing on an Illumina Hi-Seq (RiboZero capture, 150bp paired end reads). Are there any rules of thumb for how many reads I'll need to sequence to confidently assembly a majority of the transcripts?  ...
rna-seq sequencing written 4.4 years ago by alex.rubinsteyn130 • updated 4.4 years ago by Biostar ♦♦ 20
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Protein variant notation for an inserted stop codon?
... How do I annotate the protein effect of an in-frame insertion of a "TAG" stop codon inside a cDNA sequence?  Typically, I would annotate an insertion with something like: p.K2_L3insQ (insert a glutamine between the lysine at position 2 and the leucine at position 3). If the inserted sequence result ...
variant mutation notation written 4.4 years ago by alex.rubinsteyn130 • updated 4.4 years ago by Devon Ryan90k
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Comment: C: Can APPRIS be used to determine principal isoforms in older Ensembl releases?
... Thanks Denise,  Do you think the principal transcripts in APPRIS would still exist in e.g. Ensembl release 54? ...
written 4.6 years ago by alex.rubinsteyn130
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Comment: C: Is it possible for a genetic locus to be "in" a gene but not within the bounds o
... The inclusion of regulatory regions seems, I think, different from how Ensembl defines genes. It's also confusingly vague: would you include all eQTLs as part of a gene? ...
written 4.6 years ago by alex.rubinsteyn130
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Is it possible for a genetic locus to be "in" a gene but not within the bounds of any transcript?
... I'm wondering, from the point of view of an annotation library like Ensembl, does it make any sense for a locus to be inside a gene but not inside any transcript?  ...
ensembl written 4.6 years ago by alex.rubinsteyn130 • updated 4.6 years ago by Istvan Albert ♦♦ 80k
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Can APPRIS be used to determine principal isoforms in older Ensembl releases?
... I'm working with variants which were aligned against an older genome (hg19) and, thus,annotated using an older Ensembl release (75). Would it still make sense to use APPRIS to determine the principal isoform for each coding variant? Are Ensembl IDs stable across releases (in the sense that a particu ...
appris ensembl transcripts written 4.6 years ago by alex.rubinsteyn130 • updated 3.8 years ago by crisime180

Latest awards to alex.rubinsteyn

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Are EC50, Kd, and IC50 values for MHC binding assays comparable?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Are EC50, Kd, and IC50 values for MHC binding assays comparable?

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