Moderator: Ian

gravatar for Ian
Ian5.6k
Reputation:
5,640
Status:
Trusted
Location:
University of Manchester, UK
Website:
http://personalpages.m...
Twitter:
IanDcalling
Scholar ID:
Google Scholar Page
Last seen:
2 months, 3 weeks ago
Joined:
9 years, 11 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 • 434 results • page 2 of 44 • next >
1
vote
1
answer
708
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 21 months ago by Ian5.6k
0
votes
1
answer
425
views
1
answers
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 21 months ago by Ian5.6k
1
vote
4
answers
803
views
4
answers
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 22 months ago by Ian5.6k
2
votes
2
answers
1.1k
views
2
answers
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 2.2 years ago by Ian5.6k
5
votes
2
answers
1.1k
views
2
answers
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 2.3 years ago by Ian5.6k
0
votes
2
answers
1.1k
views
2
answers
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 2.4 years ago by Ian5.6k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Biological significance of Fold_enrichment in macs2
... Sorry I missed your question, but Devon was absolutely right. ...
written 2.4 years ago by Ian5.6k
2
votes
2
answers
3.2k
views
2
answers
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 2.5 years ago by Ian5.6k
2
votes
1
answer
1.3k
views
1
answers
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 2.5 years ago by Ian5.6k
0
votes
1
answer
759
views
1
answers
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 2.5 years ago by Ian5.6k

Latest awards to Ian

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?
Teacher 5 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 Weeder 2.0 - motif discovery tool updated
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
Great Question 8 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 8 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Pundit 15 months ago, created a comment with more than 10 votes. For C: Sequence Length Distribution From A Fastq File
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Resource For Gff-Files?
Great Question 15 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 16 months ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Resource For Gff-Files?
Good Question 20 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 24 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 2.1 years ago, created a question with more than 1,000 views. For How to add gene annotation to a UCSC assembly hub?
Student 2.1 years ago, asked a question with at least 3 up-votes. For How to add gene annotation to a UCSC assembly hub?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Resource For Gff-Files?
Great Question 2.2 years 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 2.2 years ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Great Question 2.3 years 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 2.5 years ago, created an answer that has been accepted. For A: How to add gene annotation to a UCSC assembly hub?
Epic Question 2.5 years ago, created a question with more than 10,000 views. For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1026 users visited in the last hour