User: chrisclarkson100

Reputation:
50
Status:
Trusted
Location:
European Union
Last seen:
5 hours ago
Joined:
3 years, 3 months ago
Email:
c***************@yahoo.co.uk

Posts by chrisclarkson100

<prev • 87 results • page 1 of 9 • next >
0
votes
0
answers
147
views
0
answers
can one assess the how well the output of ChromHMM fits the data given to it?
... I have implemented an analysis with ChromHMM, with many histone marks as input. I used a range of different numbers for states and assessed the output of each. for i in {1..10} do java -mx1600M -jar ~/ChromHMM/ChromHMM.jar LearnModel -p 6 ChromHMM_binary ${i}_e $i mm9 done Across a ...
chip-seq chromhmm written 9 weeks ago by chrisclarkson10050
1
vote
3
answers
388
views
3
answers
Answer: A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... After contacting SRA. It appears that they have done away with the 'SRX' experiment directory: *"The size of the SRA prevents the use of an FTP tree centered around experiments and had to be taken down. If you really need to use the old method of an FTP tree then look at the Runs organized by a stud ...
written 9 weeks ago by chrisclarkson10050
0
votes
3
answers
388
views
3
answers
Comment: C: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... Thank you for this information but when I try to access the following ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX134/SRX1342333 (also not available). I then search it on the SRA database: SRX1342333 like you did and it is available.... However I just can't seem to access ...
written 10 weeks ago by chrisclarkson10050
6
votes
3
answers
388
views
3
answers
SRA has done away with SRX experiment directories on FTP site: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/.... might be temporarily down
... I have been trying all day to access different SRA files on the GEO database but keep being met with '404' kind of error- stating that the site is down. I have tried on two separate computers and get the same result... taking the following path as an example: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sr ...
software error written 10 weeks ago by chrisclarkson10050
0
votes
1
answer
184
views
1
answer
PFM for CTCF in mm9 extremely difficult to find- or does one exist?
... Apologies for the naive question but I am new to the field of Position Frequency matrices (PFMs). I am trying to find a PFM for CTCF binding in the mm9 version of the mouse genome... I have searched JASPAR, TRANSFAC and http://ccg.vital-it.ch/pwmtools/pwmbrowse.html. None of the databases in these ...
assembly written 3 months ago by chrisclarkson10050 • updated 3 months ago by jared.andrews07540
0
votes
2
answers
292
views
2
answers
Comment: C: separating bed file into separate files for every 100000 base pairs
... Hi, thank you for this, In your GitHub example you input: first_fit.py hg19.gapped_extents.bed 100 1e8 I have tried your example on my own data and it looks encouraging but I am looking to write the lines within a certain base pair range to separate files. This script does not seem to do that. The ...
written 3 months ago by chrisclarkson10050
5
votes
2
answers
292
views
2
answers
separating bed file into separate files for every 100000 base pairs
... I have a really large bed file (24 GB) and I want to separate it into different files for every million base pairs. I have done it the pure programming way but this really slow #python file=open(sys.argv[1], 'r') lines=file.readlines() #print lines start=[] end=[] chr=[] ...
assembly written 3 months ago by chrisclarkson10050
6
votes
2
answers
301
views
2
answers
gc content file for human genome large and difficult to parse into separate chromosome files
... I have just downloaded the following 'gc content' documenting file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/hg19.gc5Base.txt.gz The file contains data for all chromosomes in hg19. **it is not in bed format which makes it difficult to parse in terms of separating into chromosome files ** ...
assembly written 4 months ago by chrisclarkson10050 • updated 4 months ago by igor5.0k
0
votes
1
answer
312
views
1
answers
Comment: C: sam2bed processing paired-end data and producing unexpectedly short intervals in
... I don't actually have this file in BAM format... I mapped it directly to sam format with: bowtie2 -x mm9 --very-sensitive -p 8 -1 SRR1.fastq -2 SRR2.fastq -S out.sam so the only file here is in sam format ...
written 4 months ago by chrisclarkson10050
0
votes
1
answer
312
views
1
answers
Comment: C: sam2bed processing paired-end data and producing unexpectedly short intervals in
... I should also mention that I have previously used a script to account for the paired end read data: https://github.com/homeveg/nuctools/extend_PE_reads.pl but this did not seem to make a difference to the intervals, the vast majority of which are < 147. Hence I was worried that it might be a ste ...
written 4 months ago by chrisclarkson10050

Latest awards to chrisclarkson100

Scholar 9 weeks ago, created an answer that has been accepted. For A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
Popular Question 12 weeks ago, created a question with more than 1,000 views. For blastn linux command specify database
Supporter 3 months ago, voted at least 25 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 6 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Great Question 10 months ago, created a question with more than 5,000 views. For what are single copy genes?
Popular Question 10 months ago, created a question with more than 1,000 views. For sequence BLASTed against itself.... why?
Great Question 10 months ago, created a question with more than 5,000 views. For venn diagram for gene lists using R
Popular Question 10 months ago, created a question with more than 1,000 views. For what are single copy genes?
Popular Question 19 months ago, created a question with more than 1,000 views. For what are single copy genes?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For what are single copy genes?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For venn diagram for gene lists using R
Student 3.0 years ago, asked a question with at least 3 up-votes. For venn diagram for gene lists using R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 911 users visited in the last hour