Moderator: Ian

gravatar for Ian
Ian5.3k
Reputation:
5,260
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Trusted
Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
Scholar ID:
Google Scholar Page
Last seen:
19 hours ago
Joined:
8 years, 5 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 • 429 results • page 1 of 43 • next >
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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 6 weeks ago by Ian5.3k
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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 3 months ago by Ian5.3k
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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 3 months ago by Ian5.3k
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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 3 months ago by Ian5.3k
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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 4 months ago by Ian5.3k
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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 4 months ago by Ian5.3k
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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 4 months ago by Ian5.3k
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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 9 months ago by Ian5.3k
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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 10 months ago by Ian5.3k
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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 11 months ago by Ian5.3k

Latest awards to Ian

Popular Question 28 days ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 3 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 6 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 7 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 7 months ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 9 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 9 months ago, created an answer that has been accepted. For A: 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
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Scholar 12 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Epic Question 12 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 14 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 17 months ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Teacher 18 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 19 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 19 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 20 months ago, created a question with more than 5,000 views. For How To Plot Read Coverage Over Many Different Genomic Regions?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Appreciated 22 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Epic Question 22 months ago, created a question with more than 10,000 views. For What Is The Difference Between Samtools Mpileup And Pileup
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

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