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Moderator: Ian

gravatar for Ian
Ian ♦ 5.2k
Reputation:
5,190
Status:
Trusted
Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
Scholar ID:
Google Scholar Page
Last seen:
5 days, 22 hours ago
Joined:
8 years, 1 month 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 • 425 results • page 1 of 43 • next >
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Answer: A: Using HTseq-count for Pseudomonas Aeruginosa data
... When you run htseq-count check that the -i flag is set to ID (-i ID) and not 'gene_id', which is the GTF default. ...
written 11 days ago by Ian ♦ 5.2k
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Answer: A: how to determine bacteria relatedness from two variant calls
... You could try SNPRelate (https://bioconductor.org/packages/release/bioc/html/SNPRelate.html). You can create a PCA plot of the samples based on their VCF files. ...
written 11 days ago by Ian ♦ 5.2k
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Answer: A: How find correlations between ChIP-seq tracks?
... Seqminer (https://sourceforge.net/projects/seqminer/) is old (2012), but allows you to download the genes from the different clusters you observe, something I have not managed to do with Deeptools. ...
written 24 days ago by Ian ♦ 5.2k
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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 5 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 6 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 7 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 7 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 8 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 8 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 8 months ago by Ian ♦ 5.2k

Latest awards to Ian

Great Question 11 weeks 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 3 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 3 months ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
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
Scholar 5 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Great Question 6 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 8 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Scholar 8 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Epic Question 8 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 11 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 13 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
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
Popular Question 15 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 15 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 16 months ago, created a question with more than 5,000 views. For How To Plot Read Coverage Over Many Different Genomic Regions?
Appreciated 17 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Epic Question 18 months ago, created a question with more than 10,000 views. For What Is The Difference Between Samtools Mpileup And Pileup
Popular Question 18 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 19 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Great Question 19 months ago, created a question with more than 5,000 views. For Extracting Paired-End Reads Sitting In Different Chromosomes
Appreciated 20 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
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