User: i.sudbery

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i.sudbery1.5k
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IanSudbery
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Posts by i.sudbery

<prev • 141 results • page 1 of 15 • next >
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Comment: C: RNASeq data normalisation affected by genes with large number of read counts
... Take a look at an MDS plot of your data, is one of these replicates massively outlying? In any case it seems you need a stronger normalisation than you are doing. Hand-calculated TPMs generally use the total number of reads in a sample, but no mainstream RNAseq package uses this, in fact they exclud ...
written 13 days ago by i.sudbery1.5k
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Answer: A: RNASeq data normalisation affected by genes with large number of read counts
... Firstly 0.6 is not a good correlation. Secondly, think about the normalisation you want: * **if you are looking at changes between conditions** (and it appears you are because you are talking about genes which are up and genes which are down), you need to do between sample normalisation, but betw ...
written 14 days ago by i.sudbery1.5k
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Comment: C: Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?
... Sorry, cf means "compared with" https://en.wikipedia.org/wiki/Cf. ...
written 26 days ago by i.sudbery1.5k
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Answer: A: Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?
... You might like to try DaPars: http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html Its the tool i've used the most, although its never led to any significant discovery for us. I'd be interested in how you get on cf roar. ...
written 27 days ago by i.sudbery1.5k
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Answer: A: Tools for demultiplexing a large fastq file based on random in-line barcodes
... The new version of [UMI-Tools][1] now has mechanisms for dealing with data that has inline cell barcodes. [1]: https://github.com/CGATOxford/UMI-tools ...
written 28 days ago by i.sudbery1.5k
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Tool: UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
... We are proud to announce the release of UMI-Tools 0.5. ![enter image description here][1] UMI-tools provides error aware tools for dealing with short random oligos (Unique Molecular Identifiers/Random Molecular Tags). The novel, error corrected UMI deduplication algorithm was published [here][2]. ...
umi rna-seq single cell tool written 29 days ago by i.sudbery1.5k
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Comment: C: Download SAM/BAM files from SRA takes ages!!!
... The solution is to use ENA rather than SRA - everything apart from the controlled access stuff is mirrored accross and ENA store the raw fastq, which can be downloaded directly by ascp. ...
written 7 weeks ago by i.sudbery1.5k
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Comment: C: Download SAM/BAM files from SRA takes ages!!!
... My biggest problem with this is that for at least fastq data, the rate limiting step is generally the dump rather than the actual download. ...
written 7 weeks ago by i.sudbery1.5k
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Comment: C: Download SAM/BAM files from SRA takes ages!!!
... I once broke the universities connection to backbone when downloading many files simultaneously on unthrottled ascp. ...
written 7 weeks ago by i.sudbery1.5k
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Comment: C: Pysam changes bam format when printing
... To answer your actaul question... Its like this because this is what is actually stored in a BAM file, which are not quite just compressed SAM files. pysam acts as a wrapper around the htslib c library, which is the same thing samtools uses, and that returns a c-structure representing the read rathe ...
written 3 months ago by i.sudbery1.5k

Latest awards to i.sudbery

Supporter 29 days ago, voted at least 25 times.
Appreciated 29 days ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
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?
Teacher 3 months 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?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 4 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?
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?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Popular Question 6 months ago, created a question with more than 1,000 views. For StringTie: To use a reference gene-set or not?
Scholar 6 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Guru 6 months ago, received more than 100 upvotes.
Centurion 8 months ago, created 100 posts.
Scholar 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 11 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 12 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
Scholar 12 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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