User: Bella_p

gravatar for Bella_p
Bella_p50
Reputation:
50
Status:
Trusted
Location:
Last seen:
1 month, 2 weeks ago
Joined:
9 months, 1 week ago
Email:
b********@gmail.com

Posts by Bella_p

<prev • 29 results • page 1 of 3 • next >
0
votes
1
answer
134
views
1
answers
Comment: C: How to add Unique Peak ID to a bed file created from MACS for HOMER analysis
... Thanks! I thought so, and needed clarification. Can I ask you about the -size argument? I'm doing ChipSeq analysis, what is the common size to use? ...
written 10 weeks ago by Bella_p50
4
votes
1
answer
134
views
1
answer
How to add Unique Peak ID to a bed file created from MACS for HOMER analysis
... Hi all, I'm new with using MACS and HOMER. I have created a bed file using MACS, and got 5 columns, for example: chr1 770811 771252 MACS_peak_1 93.92 chr1 851512 851790 MACS_peak_2 57.31 chr1 920907 921486 MACS_peak_3 207.37 chr1 946784 946982 MACS_peak_4 73.24 Does anyone knows ...
macs homer chip-seq written 10 weeks ago by Bella_p50 • updated 10 weeks ago by b.nota4.0k
0
votes
2
answers
213
views
2
answers
Comment: C: Where can I find GV .genome files for igvtools
... I understand, so one of those files I downloaded actually contains what you wrote. Thanks a lot! ...
written 10 weeks ago by Bella_p50
5
votes
2
answers
213
views
2
answers
Where can I find GV .genome files for igvtools
... Hi, I'd like to use igvtools count on the command line. According to the IGV website, it is possible with: "id, or a full path to a .chrom.sizes or an IGV .genome file. " I can't find any IGV .genome file for the command. I downloaded a zip file containing 3 files: hg18_cytoBand.txt ...
chip-seq igv written 10 weeks ago by Bella_p50 • updated 10 weeks ago by dariober9.2k
0
votes
1
answer
146
views
1
answers
Comment: C: Using igvtools count with bam anf bam.bai files
... Thanks! Is it needed for igvtools count? or IGV visualization? and how is it different from .bed file? ...
written 11 weeks ago by Bella_p50
4
votes
1
answer
146
views
1
answer
Using igvtools count with bam anf bam.bai files
... Hi all, I'm a beginner with using igv, and I have .bam file and it's .bam.bai file, that I created using samtools index. Is igvtools count accepts both files (bam and bam.bai)? according to the wesbite: "Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed." can't see anyt ...
igvtools chip-seq sequencing written 11 weeks ago by Bella_p50 • updated 11 weeks ago by h.mon15k
1
vote
0
answers
153
views
0
answers
How to get the statistics of bowtie alignment into a file?
... Hi, I'm using bowite for alignment with the following script: ${bowtie_source} --best --sam ${ref_genome} ${fastq_file} | ${samtools} view -bS - | ${samtools} sort -o ${target_dir}/${sample_name}.bam and on the terminal I get the statistics: # reads processed: 12641952 # reads wi ...
chip-seq bowtie written 11 weeks ago by Bella_p50
0
votes
1
answer
216
views
1
answers
Comment: C: Merging list of bam files with samtools merge
... Thanks, it won't solve my problem, but it seems that I did confused the output input. The python script is long, so I wrote only the relevant lines from it. It does other things then just merge, so it's easier for me to send from it to simple bash script for merge, and the rest, with python. ...
written 11 weeks ago by Bella_p50
0
votes
1
answer
216
views
1
answers
Comment: C: Merging list of bam files with samtools merge
... my python script is: bam_files_list = [file for file in os.listdir(bam_file_path) if file.endswith(".bam")] subprocess.call([".merge_and_remove_dup.sh", bam_files_list, sample_name],shell=False) Then the bash command. So you say I need to convert the list to sequence of strings (names of th ...
written 11 weeks ago by Bella_p50
1
vote
1
answer
216
views
1
answer
Merging list of bam files with samtools merge
... Hi, I want to merge list of bam files (after I already sorted them previously) using samtools merge. I have a list of bam files that I want to sent from python to the following command in bash: ${samtools} merge - ${bam_source}/${sample_name}.merged.bam Will samtools work with list from pytho ...
python samtools bash written 11 weeks ago by Bella_p50 • updated 11 weeks ago by h.mon15k

Latest awards to Bella_p

Student 9 months ago, asked a question with at least 3 up-votes. For Recommended book and courses to study Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 669 users visited in the last hour