User: mary.a.wood.91

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Posts by mary.a.wood.91

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Comment: C: Find stop codon for coding transcript in gencode gtf if not given?
... My curiosity is why so many protein coding transcripts are poorly annotated (i.e. lack an annotated start or stop codon). Around 1/3 of the transcripts described as protein coding in the gencode 27 release GTF file lack a start codon feature, stop codon feature, or both. Why is it that these feature ...
written 12 months ago by mary.a.wood.9110
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Comment: C: Find stop codon for coding transcript in gencode gtf if not given?
... This was just one example - but this means the annotation is incomplete, right? And this seems to be the case for a lot of transcripts. Why do these annotations end up incomplete, and why so often? Is resolving a stop codon fairly difficult? ...
written 12 months ago by mary.a.wood.9110
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Find stop codon for coding transcript in gencode gtf if not given?
... I'm trying to determine how to find the stop codon position for a protein coding transcript if there is no stop codon feature listed for it in a gencode gtf file. For example, an insulin transcript (ENST00000421783.1) is listed as a protein coding transcript in the gencode GRCh37 gtf, and has star ...
gtf ensembl codon stop gencode written 12 months ago by mary.a.wood.9110 • updated 12 months ago by Istvan Albert ♦♦ 78k
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Comment: C: Is it okay to realign and subsequently process fastq files that were converted f
... Okay, thanks so much for your help! ...
written 17 months ago by mary.a.wood.9110
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Comment: C: Is it okay to realign and subsequently process fastq files that were converted f
... Thanks Istvan! You don't think there will be any issues with the quality scores, for example when it comes time to call variants? ...
written 17 months ago by mary.a.wood.9110
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Comment: C: Is it okay to realign and subsequently process fastq files that were converted f
... It's not necessarily out of the question, but difficult. I wasn't the one directly given the data, and my supervisor who received the files is having difficulty reaching those who generated the data. I was hoping to be able to move forward with analysis, but I wanted to try get a general feel for ho ...
written 17 months ago by mary.a.wood.9110
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Is it okay to realign and subsequently process fastq files that were converted from processed BAM files?
... I have been given BAM files from a collaborator that have already gone through processing, but I want to incorporate this data set into a larger analysis for which I have a standard protocol for taking files from fastq through somatic variant calling (roughly similar to GATK's best practices). I am ...
fastq alignment recalibration bwa bam written 17 months ago by mary.a.wood.9110 • updated 17 months ago by Istvan Albert ♦♦ 78k

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