User: James Ashmore

gravatar for James Ashmore
James Ashmore1.5k
Reputation:
1,470
Status:
Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
11 hours ago
Joined:
2 years, 7 months ago
Email:
j******@icloud.com

I am a PhD student in Simon Tomlinson's research group at the MRC Centre for Regenerative Medicine. My interests lie in the biology of reprogramming, and developing methods to analyse the reprogramming process.

Posts by James Ashmore

<prev • 174 results • page 1 of 18 • next >
0
votes
0
answers
70
views
0
answers
Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... MACS2 will scale the number of reads in your treatment sample down to the number in your control sample. That means you can provide any number/combination of treatment and control samples and MACS2 will scale them accordingly. ...
written 1 day ago by James Ashmore1.5k
0
votes
1
answer
138
views
1
answers
Comment: C: A code for splitting FASTA file, No output is written for the file
... Could you explain what your desired format / output extension is? It might be easier to use seqkit to split the sequence and then write a much simpler shell script to do the post-processing? ...
written 1 day ago by James Ashmore1.5k
0
votes
2
answers
117
views
2
answers
Answer: A: MACS2 with multiple replicates
... As far as I'm aware it just pools the replicates. ...
written 10 days ago by James Ashmore1.5k
0
votes
1
answer
82
views
1
answers
Comment: C: Questions about LB field in SAM specification for PCR duplicate removal
... What do you define as library? ...
written 18 days ago by James Ashmore1.5k
0
votes
1
answer
152
views
1
answers
Answer: A: number of MAPQ=0 reads or alignments in BWA MEM output
... Maybe try using bioawk: samtools view input.bam | bioawk -c sam '$mapq == 0 {sum += 1} END {print sum}' ...
written 18 days ago by James Ashmore1.5k
0
votes
1
answer
82
views
1
answer
Questions about LB field in SAM specification for PCR duplicate removal
... Should the LB field in the SAM specification refer to the library preparation for the sample, or the library preparation carried out by the sequencing centre? Say I have a sample sequenced on multiple lanes of a single flowcell/machine, should they have the same library name? Or what if I have a sam ...
sam markduplicates written 18 days ago by James Ashmore1.5k
1
vote
2
answers
112
views
2
answers
Answer: A: Trim FASTA header in multifasta file
... No access to Windows power shell, but this python script should do it: with open('output.fasta', 'w') as outfile: with open('input.fasta', 'r') as infile: for line in infile: if line.startswith('>'): line = line[0:99] + '\n' ...
written 18 days ago by James Ashmore1.5k
0
votes
0
answers
147
views
0
answers
Comment: C: MACS2 produces different results using BAMPE and BEDPE
... Hmm okay I'm not sure, maybe best to post an issue to the MACS GitHub repository (https://github.com/taoliu/MACS/issues) or the MACS Google group (https://groups.google.com/forum/#!forum/macs-announcement). Tao Liu will obviously know more about the inner workings. ...
written 18 days ago by James Ashmore1.5k
0
votes
0
answers
147
views
0
answers
Comment: C: MACS2 produces different results using BAMPE and BEDPE
... Can you look at the .xls file MACS2 produces and see if the number of reads counted is different between your BAMPE and BEDPE files? My guess is that with the BEDPE format you're only using reads which are properly paired to measure fragment size / pileup. With the BAMPE format it's using only the p ...
written 18 days ago by James Ashmore1.5k
0
votes
2
answers
152
views
2
answers
Comment: C: Divide each fasta sequence into fragments of 200 nucleotides
... Ah yes thanks for correcting me ...
written 20 days ago by James Ashmore1.5k

Latest awards to James Ashmore

Commentator 22 days ago, created a comment with at least 3 up-votes. For C: Using getopt module to parse and define command line arguments in python
Scholar 26 days ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Scholar 27 days ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Popular Question 3 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 3 months ago, created a question with more than 1,000 views. For How can I programmatically download the GEO DataSets of a given accession?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Using getopt module to parse and define command line arguments in python
Student 9 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Student 10 months ago, asked a question with at least 3 up-votes. For Resources to understand regression models for count data
Guru 10 months ago, received more than 100 upvotes.
Appreciated 10 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Run multiple fastq.gz files with FastQC and yield single report?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.
Student 12 months ago, asked a question with at least 3 up-votes. For Resources to understand regression models for count data
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Centurion 13 months ago, created 100 posts.
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Run multiple fastq.gz files with FastQC and yield single report?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 491 users visited in the last hour