Moderator: Ian

gravatar for Ian
Ian5.5k
Reputation:
5,510
Status:
Trusted
Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
Scholar ID:
Google Scholar Page
Last seen:
4 weeks ago
Joined:
9 years, 3 months ago
Email:
d***********@gmail.com

Member of the Faculty of Life Science's bioinformatics core facility.

.

http://www.youtube.com/user/ManchesterBCF/videos?view=1&flow=grid for video tutorials.

.

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.

.

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 >
0
votes
0
answers
97
views
0
answers
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 10 weeks ago by Ian5.5k
0
votes
0
answers
97
views
0
answers
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 10 weeks ago by Ian5.5k
1
vote
0
answers
97
views
0
answers
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 10 weeks ago by Ian5.5k • updated 10 weeks ago by genomax73k
3
votes
2
answers
183
views
2
answers
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 4 months ago by Ian5.5k
0
votes
2
answers
2.7k
views
2
answers
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 8 months ago by Ian5.5k
0
votes
1
answer
607
views
1
answers
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 11 months ago by Ian5.5k
1
vote
4
answers
372
views
4
answers
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 13 months ago by Ian5.5k
0
votes
2
answers
939
views
2
answers
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 13 months ago by Ian5.5k
1
vote
3
answers
700
views
3
answers
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 14 months ago by Ian5.5k
1
vote
1
answer
552
views
1
answers
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 14 months ago by Ian5.5k

Latest awards to Ian

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
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
Pundit 7 months ago, created a comment with more than 10 votes. For C: Sequence Length Distribution From A Fastq File
Epic Question 9 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 13 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 16 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 17 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 18 months ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 19 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 20 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Great Question 20 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
Epic Question 22 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Scholar 22 months ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
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
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Bioinformatics "Cheat Sheet"
Popular Question 2.1 years 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 2.3 years ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Download Genomic Ranges From A List Of Coordinates Via Web

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1325 users visited in the last hour