User: Jonathan Crowther

Reputation:
180
Status:
Trusted
Location:
Leuven/Dublin
Website:
https://twitter.com/Jc...
Twitter:
jcrow06
Last seen:
2 years, 9 months ago
Joined:
6 years ago
Email:
j*****************@mail.dcu.ie

Currently studying for a PhD in Biomedical Science. M.Sc in Bioinformatics B.Sc Biopharmaceutical Science

Posts by Jonathan Crowther

<prev • 25 results • page 1 of 3 • next >
3
votes
0
answers
1.1k
views
0
answers
Methylation Extractor report missing Chr annotation
... Hi there, So I have recieved some Bismark output files: Bismark (SAM/BAM) Mbias files & Plots Methylation Extractor reports   The documentation is very good and I have a good understanding of all the files however in my data from the Methylation extractor there are several sites that are n ...
methylationextractor bs-seq bismark written 3.8 years ago by Jonathan Crowther180
0
votes
2
answers
14k
views
2
answers
Comment: C: Combining The Paired Reads From Illumina Run
... Works a treat, Thanks Eric! ...
written 4.0 years ago by Jonathan Crowther180
0
votes
2
answers
6.0k
views
2
answers
Comment: C: Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression d
... Hi Johanna, This GAF file is perfect! Cheers     ...
written 4.1 years ago by Jonathan Crowther180
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Enrichment determination from random sampling
... Great, thanks for the confirmation! ...
written 4.1 years ago by Jonathan Crowther180
8
votes
1
answer
1.2k
views
1
answer
Enrichment determination from random sampling
... Hi all, I would like to know if my approach makes sense or not. I have a count of histone mark peaks (Encode BigWig files) in an 80Kb window from hg19. I have sampled 1000 positions (80Kb in length) of hg19 and generated a null empirical distribution based on the counts of peaks from each of the ...
R statisitics sampling distribution written 4.1 years ago by Jonathan Crowther180 • updated 4.1 years ago by Devon Ryan88k
2
votes
1
answer
2.6k
views
1
answer
Multiplex/DeMultiplexing of illumina RNAseq Single End
... Is there a way to identify if the RNASeq data has already undergone demultiplexing? I have received files which have been run on 4 lanes and so I have 4 .fastq.gz files for each sample. I know I can compare the qualities of these to ensure there is no lane specific bias but can I figure out from t ...
rnaseq multiplexing illumina written 4.3 years ago by Jonathan Crowther180 • updated 4.3 years ago by Istvan Albert ♦♦ 79k
2
votes
1
answer
4.7k
views
1
answer
Illumina adapter identification
... Hi guys, I have a question about adapter identification. I have the raw fastq.tar.gz files from an RNAseq experiment. I am trying to replicate the pre-processing of a service provider as a learning experience. I have run the FastQC and see that the quality is good and generally all seems correct. ...
adapters illumina rna-seq written 4.3 years ago by Jonathan Crowther180 • updated 4.3 years ago by geek_y9.3k
5
votes
3
answers
30k
views
3
answers
Answer: A: from .BAM to .BAI using samtools
... You need to point the results to a file to create this: So for one file it would be  samtools index file.bam file.bam.bai See this link for a great description: Here     In your case with many bam files I would do it in a shell script as follows: #!/bin/bash for i in *.bam do echo "Inde ...
written 4.5 years ago by Jonathan Crowther180
0
votes
2
answers
4.1k
views
2
answers
Comment: C: Graph of BED data on Chromosomes
... This method looks great and doesn't require extra coding in R! Nice Alex! ...
written 4.6 years ago by Jonathan Crowther180
1
vote
2
answers
4.1k
views
2
answers
Answer: A: Graph of BED data on Chromosomes
... If you have some experience in R you could plot some nice karyograms with a plot as a line or you can also include the cytoband with a marker above the chromosome. I think they look quite nice and would be useful for you. Everything you need is here but if you want some additional help just messa ...
written 4.6 years ago by Jonathan Crowther180

Latest awards to Jonathan Crowther

Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Qual Scores In 1000 Genomes Vcf File
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Frma Normalization Via Insilicodb
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Add Additional Panes To A Clustering Heatmap Plot Created With R
Student 3.5 years ago, asked a question with at least 3 up-votes. For Enrichment determination from random sampling
Popular Question 4.1 years ago, created a question with more than 1,000 views. For RNAseq Log2Fold Change and the 2-Delta Ct fold change
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How To Add Additional Panes To A Clustering Heatmap Plot Created With R
Supporter 4.5 years ago, voted at least 25 times.
Autobiographer 5.3 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1744 users visited in the last hour