User: i.sudbery

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i.sudbery970
Reputation:
970
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Trusted
Location:
Sheffield, UK
Twitter:
IanSudbery
Last seen:
3 hours ago
Joined:
1 year, 10 months ago
Email:
i********@sheffield.ac.uk

Posts by i.sudbery

<prev • 106 results • page 1 of 11 • next >
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Answer: A: Gene list overlap - Null distribution
... As was mentioned by @Lars Juhl Jensen, the standard null distribution for two gene lists is the hypergeometric distribution. However, this assumes that all genes are independent and equally likely to show up. There are several reasons why this might not be the case: * Longer genes are more likely ...
written 10 days ago by i.sudbery970
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Comment: C: Publicly available RNA-seq data of neurons from human
... GTEx has brain data, but not specifically neuron data. ...
written 11 days ago by i.sudbery970
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Comment: C: mapping read is low for miRNA data after trimming
... Its been a while since I last did miRNA analysis, but when I did, the size distribution was pretty tight around 22nt. Maybe we didn't use the Illumina prep. This was the size distribution on the last analysis I did. ![][1] In fact, I highly recommend the [SequenceImp][2] miRNA precessing pipeline. ...
written 13 days ago by i.sudbery970
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Comment: C: HISAT2 or Tophat2
... Another thing that should be considered is how robust the results are to different parameters. In the Baruzzo study, almost all the aligners could be configured to give good results, but they differed in the performance of the default options, with STAR looking pretty good in those terms. I have to ...
written 13 days ago by i.sudbery970
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Comment: C: mapping read is low for miRNA data after trimming
... Isn't 44bp a bit long for miRNAs? I would expect them to be more in the 20-29 range. I sounds like there is still something else in your reads that isn't RNA. Does your protocol have some adaptor other than the sequecing adaptor? Also you should make sure to throw out anything that doesn't contain t ...
written 13 days ago by i.sudbery970
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Comment: C: error in bowtie2 alignment
... cutadapt can be run in paired end mode and told to drop pairs where one read is shorter than a certain length. I generally drop anything shorter than 15 or 20bp ...
written 16 days ago by i.sudbery970
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Comment: C: Remote blast from biopython
... Sounds like you are using a version of biopython from before NCBI switched to https only. ...
written 17 days ago by i.sudbery970
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Comment: C: RNA-Seq raw fastq files from TCGA
... Are you sure about that? You can see the command line used to map the reads in the BAM header. Nowhere do I see anything that suggests that only reads mapping to known genes were kept? Only known genes were used when quantifying, but that's different. Fastq's only exist in the TCGA legacy archive, ...
written 18 days ago by i.sudbery970
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Comment: C: Generate more splice variant from RNA-seq data
... I'd be careful with exons that overlapped other genes - its not that its not possible, many human genes overlap, its just that there are reasons why they might also be artefacts. Is your RNA-seq stranded? I'd also want to be careful with new exons 3' of the ORF: classically we think of exon boundari ...
written 18 days ago by i.sudbery970
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Answer: A: Generate more splice variant from RNA-seq data
... In a non-model organism, I suspect much of the annotation will come from the alignment of protein sequences from other organism against the genome in order to look for homologs. Thus the annotated gene region will only contain the ORF of the gene and not the UTRs. UTRs are the worst annotated part o ...
written 18 days ago by i.sudbery970

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Centurion 16 days ago, created 100 posts.
Scholar 18 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 3 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
Scholar 5 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 5 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
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Scholar 5 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 5 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?

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