Moderator: Ian

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Ian5.5k
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Location:
University of Manchester, UK
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http://personalpages.m...
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IanDcalling
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Last seen:
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9 years ago
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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 • 431 results • page 2 of 44 • next >
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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 17 months ago by Ian5.5k
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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 18 months ago by Ian5.5k
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Comment: C: Biological significance of Fold_enrichment in macs2
... Sorry I missed your question, but Devon was absolutely right. ...
written 18 months ago by Ian5.5k
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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 19 months ago by Ian5.5k
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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 19 months ago by Ian5.5k
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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 19 months ago by Ian5.5k
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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 20 months ago by Ian5.5k
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Comment: C: BagFoot TF foot printing
... As Simon said it does have support for ATAC-seq. ...
written 20 months ago by Ian5.5k
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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. **EDITED (March 2019):** Possible alternative: https://www.ncbi.nl ...
written 20 months ago by Ian5.5k
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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 2.1 years ago by Ian5.5k

Latest awards to Ian

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Pundit 4 months ago, created a comment with more than 10 votes. For C: Sequence Length Distribution From A Fastq File
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
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
Appreciated 4 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Epic Question 6 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 10 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 13 months 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 14 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 14 months ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 15 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
Scholar 16 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
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
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Scholar 19 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Epic Question 19 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 22 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 2.0 years ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Teacher 2.1 years 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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