User: BioDH

gravatar for BioDH
BioDH0
Reputation:
0
Status:
New User
Last seen:
1 month ago
Joined:
3 years, 6 months ago
Email:
h***********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by BioDH

<prev • 8 results • page 1 of 1 • next >
0
votes
0
answers
201
views
0
answers
intersection of two GFFs
... I have two GFF files. 277(A.gff) and 1628(B.gff) regions were defined in each GFF. What I would like to know is how many regions are in the intersection of two GFFs. I used bedtools as following. bedtoolls intersect -a A.gff -b B.gff -s -wa | wc -l 124 bedtoolls intersect - ...
bedtools gff intersect written 4 months ago by BioDH0 • updated 3 months ago by Biostar ♦♦ 20
4
votes
1
answer
728
views
1
answer
Different version of Tophat gives me different number of mapped reads
... I have paired-end sequenced RNA-seq files(Illumina, fastq). I trimmed the reads by trimmomatic java -jar /trimmomatic-0.36.jar PE -threads 4 -phred33 1.fastq 2.fastq 1_trim1.fastq 1_unpaire d1.fastq 2_trim2.fastq 2_unpaired2.fastq ILLUMINACLIP:/TruSeq3-PE-2.fa:3:30:10 SLIDINGWINDOW:5:20 MIN ...
tophat alignment rna-seq written 2.2 years ago by BioDH0 • updated 2.2 years ago by swbarnes28.8k
0
votes
0
answers
1.6k
views
0
answers
Comment: C: warning message after HTSeq
... Sorry. I have changed the title. Yes, that is not DESeq2. I just got the reads using HTSeq module of puthon. ...
written 3.0 years ago by BioDH0
0
votes
0
answers
1.6k
views
0
answers
Comment: C: warning message after Deseq2
... I'm sure that is paired-end data. ...
written 3.0 years ago by BioDH0
1
vote
0
answers
1.6k
views
0
answers
warning message after HTSeq
... I have analyzed RNA-seq data with HTSeq. My command that I used is **python -m HTSeq.scripts.count -f bam -r pos -s reverse -t ORF -i group -m union input.bam my.gff > output.txt** Warning message is Warning: Mate records missing for 3752 records; first such record: . 11597356 SAM al ...
software error htseq rna-seq written 3.0 years ago by BioDH0
1
vote
1
answer
615
views
1
answer
In bowtie2, What's the difference between -q and -U option
... I'm trying to analyze NET-seq data. I don't know what should I use -q or -U option. I downloaded a fastq file which was sequenced by singled end platform. I want to align the file. What I want to know is what is the difference. -q and -U ...
alignment sequence written 3.0 years ago by BioDH0
6
votes
1
answer
1.1k
views
1
answer
Getting No. of reads from BAM by pysam (ChIP-seq)
... I'm trying to get no. of reads form (TSS ~ +500) and (-500 to pA site) of each gene. What I want to get is the no of reads of TSS proximal and pA proximal region(window = 500) If I have a bed file that contains two genes, one plus strand and the other minus strand, I was wondering if following s ...
chip-seq written 3.5 years ago by BioDH0 • updated 6 months ago by Biostar ♦♦ 20
0
votes
2
answers
1.9k
views
2
answers
deeptools installation on MacBook
... I'm trying install deeptools on my Mac. I did. ~ pip install --user deeptools Requirement already satisfied: deeptools in ./Library/Python/2.7/lib/python/site-packages Requirement already satisfied: numpy>=1.9.0 in ./Library/Python/2.7/lib/python/site-packages (from deeptools) ...
mac deeptools install written 3.6 years ago by BioDH0 • updated 3.4 years ago by inowkeren0

Latest awards to BioDH

Popular Question 3 months ago, created a question with more than 1,000 views. For Getting No. of reads from BAM by pysam (ChIP-seq)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For warning message after HTSeq
Popular Question 2.2 years ago, created a question with more than 1,000 views. For deeptools installation on MacBook

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1483 users visited in the last hour