Moderator: Ian

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Ian5.7k
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Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
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Google Scholar Page
Last seen:
1 week, 1 day ago
Joined:
10 years, 6 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 • 435 results • page 1 of 44 • next >
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Comment: C: Comparing input read subtracted ChIP-read profiles using Deeptools2
... Thank you Devon and for pointing out that I should be referring to it as Deeptools2, old habits die hard. Sample B was expected to be lower. Just to clarify, the Y-axis is explained as "the depth normalized difference in coverage", which is the relative difference in coverage after normalisation? ...
written 3 months ago by Ian5.7k
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Comparing input read subtracted ChIP-read profiles using Deeptools v3.4.3
... I have used the Deeptools2 packages to produce a plot comparing profiles of histone binding relative to gene start and ends. However the first sample only reaches about 2 on the Y axis, and the second lays around 0. So I am wondering if I am using it incorrectly? In particular the use of normalis ...
deeptools written 3 months ago by Ian5.7k
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Answer: A: found non conserved regions between 2 genomes
... Hi I used to use the ECR browser for this type of question, you can find the details at https://ecrbase.dcode.org/. Just be aware that it was last updated in 2008! But this might be useful to you. ...
written 13 months ago by Ian5.7k
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Comment: C: Help need to use information in an multiple fasta alignment (MFA) file?
... Funnily enough I had looked at it because it mentioned the use of MFA files. Unfortunately it assumes that every sequence in the file is a different species, and is a multiple alignment. Whereas my file has a many pair-wise alignments. I rerun MAUVE and the .alignment file is an almost identical ...
written 17 months ago by Ian5.7k
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Comment: C: Help need to use information in an multiple fasta alignment (MFA) file?
... Thanks. I have given Mauve a try, but I didn't get a close to what I wanted with WGvista. ...
written 17 months ago by Ian5.7k
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Help need to use information in an multiple fasta alignment (MFA) file?
... Hello. I have aligned the 88 contigs of an *E.coli* *de novo* assembly against the closest reference genome, using WGvista. The aim is to identify structural differences in the alignment, in detail. The output of WGvista is a multiple fasta alignment (MFA) file. The format gives pairwise alignm ...
fasta alignment written 17 months ago by Ian5.7k • updated 17 months ago by GenoMax95k
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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 19 months ago by Ian5.7k
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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 23 months ago by Ian5.7k
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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 2.2 years ago by Ian5.7k
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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 2.4 years ago by Ian5.7k

Latest awards to Ian

Scholar 10 months ago, created an answer that has been accepted. For A: TSS file for D.melanogaster
Popular Question 10 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Great Question 10 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
Great Question 10 months ago, created a question with more than 5,000 views. For Ion Torrent Fastq Format Type?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Great Question 13 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
Great Question 13 months ago, created a question with more than 5,000 views. For Weeder 2.0 - motif discovery tool updated
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
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
Appreciated 16 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 23 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 23 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Pundit 23 months ago, created a comment with more than 10 votes. For C: Sequence Length Distribution From A Fastq File
Epic Question 2.1 years ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 2.4 years ago, asked a question that was upvoted at least 5 times. For How Best To Add Custom Variation Track To Ucsc Browser?
Great Question 2.7 years 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 2.7 years ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 2.7 years ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 2.9 years 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

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