Moderator: Ian

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Ian5.0k
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Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
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Last seen:
5 days, 5 hours ago
Joined:
7 years, 5 months ago
Email:
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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 • 418 results • page 1 of 42 • next >
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Answer: A: How to repair *all* problems identified by FastQC?
... A good way to solve the errors (taking into account what the other said about their relevance) is to run the reads through a trimming tool, such as Trimmomatic, cutadapt, etc. Not only will poor quality reads/bases be removed, but also adapters. Often rerunning fastqc will show a vast improvement. ...
written 5 days ago by Ian5.0k
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Answer: A: Biological significance of Fold_enrichment in macs2
... The fold enrichment score compares the read/fragment count at the binding region summit against the local background model. For me it is the second most useful statistic after the qvalue. After sorting by qvalue I sort by fold enrichment. I tend to discount regions with FE < 5, as these tend t ...
written 5 days ago by Ian5.0k
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Answer: A: Features for detection of gene.
... The cis-element annotation system (CEAS) software goes into this in some detail: http://liulab.dfci.harvard.edu/CEAS/ ...
written 10 days ago by Ian5.0k
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Comment: C: How can I locate motif in DNA sequence.
... If you use the UCSC browser you can enable the Public Trackhub 'JASPAR 2018 TFBS', which is good for the following genomes: hg19, hg38, ce10, dm6, sacCer3, and araTha1. You can enter the coordinates of your sites of interest as Custom Tracks, as BED formated genome coordinates. ...
written 4 weeks ago by Ian5.0k
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Comment: C: BagFoot TF foot printing
... As Simon said it does have support for ATAC-seq. ...
written 5 weeks ago by Ian5.0k
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Answer: A: BagFoot TF foot printing
... I spent about a week (off and on) and gave up. A colleague of mine has apparently managed to get usable output; after tweaking the R code. I don't like saying bad things about peoples efforts, but the documentation was atrocious. ...
written 6 weeks ago by Ian5.0k
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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 6 months ago by Ian5.0k
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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 6 months ago by Ian5.0k
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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 6 months ago by Ian5.0k
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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 7 months ago by Ian5.0k

Latest awards to Ian

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 12 weeks 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 5 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Teacher 6 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 7 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 7 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 8 months ago, created a question with more than 5,000 views. For How To Plot Read Coverage Over Many Different Genomic Regions?
Appreciated 9 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 Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
Epic Question 10 months ago, created a question with more than 10,000 views. For What Is The Difference Between Samtools Mpileup And Pileup
Appreciated 10 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 11 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Appreciated 12 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Popular Question 12 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Popular Question 12 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?
Popular Question 15 months ago, created a question with more than 1,000 views. For Mitochondrial Genome In Chip-Seq?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Appreciated 16 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 17 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Student 19 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 19 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web

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