Moderator: Ian

gravatar for Ian
Ian5.7k
Reputation:
5,650
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Trusted
Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
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Last seen:
1 week, 5 days ago
Joined:
10 years, 1 month 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 • 433 results • page 1 of 44 • next >
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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 7 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 12 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 12 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 12 months ago by Ian5.7k • updated 12 months ago by genomax87k
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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 13 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 17 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 21 months 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 23 months ago by Ian5.7k
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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 23 months ago by Ian5.7k
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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 23 months ago by Ian5.7k

Latest awards to Ian

Scholar 5 months ago, created an answer that has been accepted. For A: TSS file for D.melanogaster
Popular Question 5 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Great Question 5 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 5 months ago, created a question with more than 5,000 views. For Ion Torrent Fastq Format Type?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Great Question 7 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 7 months ago, created a question with more than 5,000 views. For Weeder 2.0 - motif discovery tool updated
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
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
Appreciated 10 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 17 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 17 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Pundit 17 months ago, created a comment with more than 10 votes. For C: Sequence Length Distribution From A Fastq File
Epic Question 19 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 23 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 2.2 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 2.3 years ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 2.3 years ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 2.4 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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