User: hinkel2

gravatar for hinkel2
hinkel210
Reputation:
10
Status:
New User
Location:
Last seen:
2 years, 7 months ago
Joined:
3 years, 2 months ago
Email:
h******@web.de

Posts by hinkel2

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
867
views
1
answer
GESS - exon skipping scanner
... Hi! I'm trying to detect exon skipping events from my RNAseq data, following the [described workflow][1]. First, I aligned my reads to reference genome using tophat2. Output bam file was sorted using samtools and used for further analysis by GESS as recommended: **python GESS.py -i myfile_sorted.b ...
gess python exon-skipping rna-seq written 2.6 years ago by hinkel210 • updated 2.4 years ago by adglink0
0
votes
0
answers
2.8k
views
0
answers
Comment: C: Problems with Trimmomatic PE output files
... Yes, I think you're right. I completely overlooked this in the manual. How stupid... I will test again and tell you! Thanks! ...
written 2.9 years ago by hinkel210
0
votes
0
answers
2.8k
views
0
answers
Comment: C: Problems with Trimmomatic PE output files
... I repeated the trimming also with others parameters (e.g. SLIDINGWINDOW:4:15 or SLIDINGWINDOW:4:20), but it looks similar. ...
written 2.9 years ago by hinkel210
5
votes
0
answers
2.8k
views
0
answers
Problems with Trimmomatic PE output files
... Hi all! I downloaded some sra datasets using ascp as recommended (https://www.ncbi.nlm.nih.gov/books/NBK158899/) and additionally used fastq-dump on the downloaded sra-files fastq-dump --gzip --split-files file.sra and got two files (file_1.fastq.gz, file_2.fastq.gz), each 7.4 GB, as output. ...
trimmomatic adapter rna-seq fastqc written 2.9 years ago by hinkel210 • updated 2.9 years ago by genomax75k
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Problem converting bam to sam (samtools)
... Thank you! I have a 64bit system (Ubuntu 16.04 LTS) on a dual boot machine. Is this file system problem due to the FAT32 and is there an easy way to fix it? Sorry for my noob questions. ...
written 3.1 years ago by hinkel210
4
votes
1
answer
1.4k
views
5 follow
1
answer
Problem converting bam to sam (samtools)
... Hi guys! I'm new to RNAseq data analysis and related bioinformatic pipelines. I just aligned my PE-reads to genome using Tophat2: **tophat2 -p 4 -G ../Arabidopsis_thaliana.TAIR10.31.gtf ../Arabidopsis_thaliana.TAIR10.31.dna.genome PE.reads.1.fastq.gz PE.reads.2.fastq.gz** I then get the default o ...
rna-seq written 3.1 years ago by hinkel210

Latest awards to hinkel2

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2325 users visited in the last hour