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Moderator: Ian

gravatar for Ian
Ian ♦ 5.2k
Reputation:
5,150
Status:
Trusted
Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
Scholar ID:
Google Scholar Page
Last seen:
1 week, 2 days ago
Joined:
7 years, 11 months ago
Email:
d***********@gmail.com

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 • 422 results • page 1 of 43 • next >
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Answer: A: Method for creating an EMBL formatted annotated sequence?
... Thanks to the other contributors, but unfortunately the EMBL format created was not accepted by ENA. However, I have found [EMBLmyGFF3][1], which will create a valid file. The validation program can be found [HERE][2]. BED to GFF3 used [THIS][3]. [1]: https://github.com/NBISweden/EMBLmyGFF3 ...
written 3 months ago by Ian ♦ 5.2k
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Method for creating an EMBL formatted annotated sequence?
... Does anyone have a method for creating an EMBL-flatfile from a FASTA file of sequence, and a BED file of genes and repeats? The purpose is for submission of an annotate genome to the ENA. Thanks. ...
sequence embl ena written 4 months ago by Ian ♦ 5.2k
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Answer: A: What shall I do with this RNA-seq data that have no replicates?
... There might still be useful results in experiment 2, but Pvalue and fold change are only indicative at best. The results might give you leads for further lab experiments, or be impressive enough to warrant a second attempt with replication. ...
written 5 months ago by Ian ♦ 5.2k
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Comment: C: Biological significance of Fold_enrichment in macs2
... Sorry I missed your question, but Devon was absolutely right. ...
written 5 months ago by Ian ♦ 5.2k
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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 6 months ago by Ian ♦ 5.2k
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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 6 months ago by Ian ♦ 5.2k
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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 6 months ago by Ian ♦ 5.2k
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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 7 months ago by Ian ♦ 5.2k
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Comment: C: BagFoot TF foot printing
... As Simon said it does have support for ATAC-seq. ...
written 7 months ago by Ian ♦ 5.2k
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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 7 months ago by Ian ♦ 5.2k

Latest awards to Ian

Great Question 20 days 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 6 weeks ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 7 weeks ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 3 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
Scholar 3 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Great Question 4 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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Scholar 6 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Epic Question 6 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
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
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 9 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
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
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
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
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 14 months ago, created a question with more than 5,000 views. For How To Plot Read Coverage Over Many Different Genomic Regions?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Appreciated 16 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Epic Question 16 months ago, created a question with more than 10,000 views. For What Is The Difference Between Samtools Mpileup And Pileup
Popular Question 16 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 17 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
Appreciated 18 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
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