Moderator: Ian

gravatar for Ian
Ian5.5k
Reputation:
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Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
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Last seen:
1 week ago
Joined:
8 years, 11 months ago
Email:
d***********@gmail.com

Member of the Faculty of Life Science's bioinformatics core facility.

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http://www.youtube.com/user/ManchesterBCF/videos?view=1&flow=grid for video tutorials.

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I specialise in ChIP-seq analysis, but also run RNA-seq and other NGS applications. Data comes, almost exclusively from illumina sequencers, but I used to mostly analyse SOLiD sequence.

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I am interested in the analysis, organisation and presentation of genomics data. I have a special place in my heart for the hunting of transcription factor binding sites.

Posts by Ian

<prev • 431 results • page 1 of 44 • next >
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Answer: A: Which conservation score to use to measure conservation of splice sites?
... The following text is from UCSC's page on PhastCons / PhyloP ([LINK][1]). I think for the size of splice-sites that the fine grained PhyloP score might be most useful. > "PhastCons is a hidden Markov model-based method that estimates the > probability that each nucleotide belongs to a conser ...
written 7 days ago by Ian5.5k
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Comment: C: ATAC-seq: differential peaks using macs2 bdgdiff yields strange results
... The suggestion of using --SPMR goes against the author's own recommendations: https://github.com/taoliu/MACS/wiki/Call-differential-binding-events ...
written 4 months ago by Ian5.5k
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Answer: A: Sorting BAM files from HISAT2 for DEXSeq
... If in any doubt just rerun 'samtools sort'. Remember if you have multiple processors then use '-@ N', where N is the number of processor cores. ...
written 7 months ago by Ian5.5k
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Answer: A: Can renaming, copying, or moving the omics data file corrupt it?
... If you are making copies of a file, particularly if the copy is going to be downloaded off a server, then using `md5sum` will produce a hash (string of characters) that are unique to the file, and can be matched with the copy. ...
written 9 months ago by Ian5.5k
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Answer: A: How to visualize Hi-C bed file format?
... It is now possible to view this type of data as a custom track on the UCSC Browser: http://genome.ucsc.edu/goldenPath/help/interact.html ...
written 9 months ago by Ian5.5k
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Answer: A: Normalising RNA-seq samples from bam files for UCSC Genome browser visualization
... I have tackled this on a small scale by retaining SAM reads used by htseq-count (--samout), and removing those excluded from the final counts, using sed '/XF:Z:$/d;/XF:Z:__/d'. After normalisation by DESeq2 I use the scaleFactor to scale the SAM > BAM files, using bedtools genomecov (-scale). ...
written 10 months ago by Ian5.5k
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Answer: A: Using HTseq-count for Pseudomonas Aeruginosa data
... When you run htseq-count check that the -i flag is set to ID (-i ID) and not 'gene_id', which is the GTF default. ...
written 10 months ago by Ian5.5k
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Answer: A: how to determine bacteria relatedness from two variant calls
... You could try SNPRelate (https://bioconductor.org/packages/release/bioc/html/SNPRelate.html). You can create a PCA plot of the samples based on their VCF files. ...
written 10 months ago by Ian5.5k
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Answer: A: How find correlations between ChIP-seq tracks?
... Seqminer (https://sourceforge.net/projects/seqminer/) is old (2012), but allows you to download the genes from the different clusters you observe, something I have not managed to do with Deeptools. ...
written 10 months ago by Ian5.5k
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Answer: A: Method for creating an EMBL formatted annotated sequence?
... Thanks to the other contributors, but unfortunately the EMBL format created was not accepted by ENA. However, I have found [EMBLmyGFF3][1], which will create a valid file. The validation program can be found [HERE][2]. BED to GFF3 used [THIS][3]. [1]: https://github.com/NBISweden/EMBLmyGFF3 ...
written 15 months ago by Ian5.5k

Latest awards to Ian

Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Pundit 3 months ago, created a comment with more than 10 votes. For C: Sequence Length Distribution From A Fastq File
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 3 months ago, created a question with more than 5,000 views. For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
Appreciated 3 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Epic Question 5 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For How Best To Add Custom Variation Track To Ucsc Browser?
Great Question 12 months ago, created a question with more than 5,000 views. For Should the reads of biological replicates be combined for ChIP-seq peak calling?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 14 months ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 15 months ago, created a question with more than 5,000 views. For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
Scholar 15 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Great Question 16 months ago, created a question with more than 5,000 views. For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Scholar 18 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Epic Question 18 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 21 months ago, created a question with more than 1,000 views. For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis

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