Moderator: Ian

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Ian4.8k
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Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
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Last seen:
4 days, 6 hours ago
Joined:
6 years, 10 months ago
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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 • 409 results • page 1 of 41 • next >
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Answer: A: ChIP-seq Input replicate correlation
... Well, they are by definition your replicates, even if they don't look particularly similar. The difference between the two inputs might be down to coverage, unless they are already normalised. You could run S1_input (as a pseudo ChIP sample) against the S2_input (as an input), and visa versa, in ...
written 4 days ago by Ian4.8k
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Comment: C: Peak calling for broad histone-modification regions
... Looks interesting; a way of complementing traditional peak calling methods - thanks. ...
written 8 days ago by Ian4.8k
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Answer: A: Filter MACS peaks by enrichment/FDR?
... Have you considered that there are many binding regions for the protein you are investigating, some factors are ubiquitous. The FDR cut off sounds reasonable, although MACS2 suggests a q-value of 0.01 initially. I usually use FE >=10 as a cut off, but it is arbitrary. The best way is to observ ...
written 13 days ago by Ian4.8k
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Comment: C: prepare pair-ended reads for peak calling
... What 'd' values do you get? The mean fragment length for single end reads is determined by cross-correlation, and for paired-end the mean of the known fragment lengths is used. You could use the same value of 'd' by using --nomodel --extsize 200. ...
written 4 weeks ago by Ian4.8k
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Comment: C: prepare pair-ended reads for peak calling
... A BEDPE file created from the bowtie2 paired BAM file is a necessary intermediate from which you can create your BED file, as suggested above. ...
written 7 weeks ago by Ian4.8k
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Comment: C: Extract Sequence From Fasta File Using Ids From A Separate File
... http://hgdownload.cse.ucsc.edu/admin/exe/ ...
written 10 weeks ago by Ian4.8k
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Comment: C: How to extend variable length intervals to the same final length?
... Thanks for the addition. After discussing this with a colleague this morning it was pointed out that finding the mid-point of each region and then extending out works equally well. I knew I had missed something! ...
written 10 weeks ago by Ian4.8k
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Comment: C: How to extend variable length intervals to the same final length?
... Thank you for your answer! I was going to ask how it handles odd lengths. It is OK if one side has an extra base, as long as the final length is the same. ...
written 10 weeks ago by Ian4.8k
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How to extend variable length intervals to the same final length?
... I have a large set of footprint intervals that range from 11 to 25bp For the purpose of motif discovery I would like to extend all intervals to, for example, 50bp. Intervals should be extended equally from both sides. I would usually use 'bedtools slop' for fixed length intervals, but this would ...
bedtools footprint intervals slop written 10 weeks ago by Ian4.8k • updated 10 weeks ago by Alex Reynolds18k
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Answer: A: ChIP on chip array cover genome or promoter regions?
... The first one GSE54108 is not a ChIP-on-chip kit, it is gene expression: Agilent-026652 Whole Human Genome Microarray 4x44K v2 http://www.genomics.agilent.com/article.jsp?pageId=1516 The second would appear to be a promoter array, possibly -2.5 to 1kb from TSS: Agilent-014706 Human Promoter ChIP-on ...
written 3 months ago by Ian4.8k

Latest awards to Ian

Good Answer 19 days ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 4 weeks ago, created a question with more than 5,000 views. For How To Plot Read Coverage Over Many Different Genomic Regions?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Epic Question 3 months ago, created a question with more than 10,000 views. For What Is The Difference Between Samtools Mpileup And Pileup
Popular Question 3 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
Appreciated 4 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 4 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Popular Question 5 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Popular Question 5 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Popular Question 6 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Popular Question 8 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Appreciated 10 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 10 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Student 12 months ago, asked a question with at least 3 up-votes. For Illumina'S New Reduced Resolution Q (Phred) Scores - Good Or Bad?
Great Question 12 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Popular Question 12 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
Great Question 13 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Popular Question 13 months ago, created a question with more than 1,000 views. For Regular expression matching with Python and biopython SeqIO
Popular Question 13 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
Popular Question 14 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
Great Question 15 months ago, created a question with more than 5,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?

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