Moderator: i.sudbery

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i.sudbery8.2k
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Sheffield, UK
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IanSudbery
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I am a Lecturer in Bioinformatics at the University of Sheffield, where my group studies all things gene regulation, but with a particular emphasis on post-transcriptional gene regulation and RNA-processing. I am also an author of the UMI-tools, iCLIPlib, CGAT and CGAT-core packages.

Posts by i.sudbery

<prev • 728 results • page 1 of 73 • next >
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Comment: C: Generate gene level TPM from quant.sf file generated in salmon
... tx2gene = transcripts(EnsDb.Hsapiens.v86, columns=c("tx_id", "gene_name", "gene_id"), return.type="DataFrame") Should be tx2gene = transcripts(EnsDb.Hsapiens.v86, columns=c("tx_id", "gene_name", "gene_id"), ...
written 1 day ago by i.sudbery8.2k
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Comment: C: Fold change - a final explanation
... If you have a FC of 0.5, then that is a 2 fold decrease: i.e. the fold decrease is 1/FC, not -1/FC. Unless you want your 2 fold decrease to be written as -2. 1/FC is effectively changing the direction of the comparison - that is which of the two conditions is treatment and which control. ...
written 7 days ago by i.sudbery8.2k
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Comment: C: Split RNA Seq reads
... Or alternatively, if there is plenty of support (many, non-duplicate reads), then your probably looking at a novel unannotated splice junciton. ...
written 8 days ago by i.sudbery8.2k
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Comment: C: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
... Still need to be careful - almost all the gotcha's that apply to writing interleaved also apply to writing to two separate outfiles when using `samtools fastq`. ...
written 9 days ago by i.sudbery8.2k
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Answer: A: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
... BWA does not understand the `/1` and `/2` suffixes on read names. It can use "interleaved" format - that is where the file alternates between read1 and read2. However `samtools fastq` doesn't guarentee that the reads will be output in exactly interleaved order. For a start, the bam must be read na ...
written 9 days ago by i.sudbery8.2k
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Answer: A: Tophat / output without XS
... Tophat is deprecated software. Unless you have a good reason (such as replicating an old analysis) to use Tophat over more modern, accurate and actively supported software, such as STAR or HISAT2. Likewise Cufflinks is superseded by StringTie, although there hasn't actaully been a deprecation notic ...
written 9 days ago by i.sudbery8.2k
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Comment: C: Using of GSEA to compare RNA seq data with published gene sets?
... Do you mean "sign of fold change" or "signed fold change", because **signed fold change * -log10pvalue** would be a strange metric to rank on, where as "sign of fold change" makes some sense. That is if a gene had a log-fold-change of -2 and a -log10pvalue of 3, then using -3 as the score makes ...
written 9 days ago by i.sudbery8.2k
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Comment: C: Using of GSEA to compare RNA seq data with published gene sets?
... Sounds like a perfectly reasonable analysis to me. Who is objecting? Do they give a basis? Are you sure that they are objecting to the concept of the analysis and not some facet of how it was implemented? For example, one could imagine that there might be bais introduced by doing the human-mouse ...
written 10 days ago by i.sudbery8.2k
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Comment: C: Why does umi_tools dedup not write anything in the deduplicated.bam file?
... So the 16S is only about 1.5kb long, and you've sequenced with over 100M reads. If coverage is even, that means you will have 74,000 reads on every position. This is going to mean either that either you have a very large number of UMIs, or a very high duplication rate. It might be import to know - i ...
written 17 days ago by i.sudbery8.2k
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Comment: C: Why does umi_tools dedup not write anything in the deduplicated.bam file?
... The level of resource usage is more dependent on the level of duplication that it is on the total number of reads. Memory usage in particular is dependent on the maximum number of UMIs at any one position. What sort of data is this? Is it scRNA-seq? Amplicon sequencing? Exon-sequencing? ...
written 20 days ago by i.sudbery8.2k

Latest awards to i.sudbery

Appreciated 6 days ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 23 days ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 23 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 24 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Generate more splice variant from RNA-seq data
Appreciated 3 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Is there any NGS tool which produce long pairwise reads?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?

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