Moderator: Ian

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Ian4.9k
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Location:
University of Manchester, UK
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http://personalpages.m...
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IanDcalling
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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 • 412 results • page 1 of 42 • next >
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Comment: C: How to choose Trimmomatic's parameter 'MINLEN '?
... I would not go down to 10bp. Remember the shorter the read length the greater the chance of a false positive match. You could go to 25bp if you are despirate. However, looking at the numbers of reads per length I think the majority of reads are >35bp anyway. Below 35bp numbers are only in the ...
written 4 months ago by Ian4.9k
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Answer: A: Differential chip-seq peak calling using macs2
... If you have paired reads then you need to use -f BAMPE, otherwise only the 5' read of each pair will be used and cross-correlation will be used to estimate fragment length, as opposed to using the actual fragment lengths between pairs. Have you compared the 'd' value for each analysis? I haven't ...
written 4 months ago by Ian4.9k
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Answer: A: How to choose Trimmomatic's parameter 'MINLEN '?
... The lowest I select is MINLEN:35 as this was the read length Illumina sequence for a long time. The important thing is ensure the base quality is good, especially at the 3' end. I usually use SLIDINGWINDOW:4:20. I personally do not use LEADING, as it has never been a problem. Also make sure you ...
written 4 months ago by Ian4.9k
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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 5 months ago by Ian4.9k
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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 5 months ago by Ian4.9k
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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 5 months ago by Ian4.9k
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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 6 months ago by Ian4.9k
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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 6 months ago by Ian4.9k
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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 7 months ago by Ian4.9k
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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 7 months ago by Ian4.9k

Latest awards to Ian

Commentator 9 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Teacher 5 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 5 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
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 6 months ago, created a question with more than 5,000 views. For How To Plot Read Coverage Over Many Different Genomic Regions?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Popular Question 8 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
Epic Question 8 months ago, created a question with more than 10,000 views. For What Is The Difference Between Samtools Mpileup And Pileup
Appreciated 8 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 9 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Popular Question 10 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Popular Question 10 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Popular Question 11 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Popular Question 13 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Appreciated 15 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 15 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Student 17 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 17 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Teacher 17 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 17 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

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