User: Daniel Gerlach

Reputation:
30
Status:
New User
Location:
Austria
Twitter:
gerlach_d
Scholar ID:
Google Scholar Page
Last seen:
2 years, 5 months ago
Joined:
6 years, 10 months ago
Email:
d**********************@gmail.com

Bioinformatics and genomics research for drug development.

Posts by Daniel Gerlach

<prev • 4 results • page 1 of 1 • next >
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Why does submitting high-throughput sequence data to GEO from an Amazon EC2 instance produce the error "Could not read reply from control connection -- timed out" ?
... I am following the instruction mentioned on [Submit to GEO][1] to upload about 83G of RNA-seq data in gzipped form to the GEO FTP server. I was first using the following command, but the connection had a time-out after every file: ncftpput -B 33554432 -z -u 'username' -p 'password' -v -R \ ...
geo ftp next-gen written 2.8 years ago by Daniel Gerlach30 • updated 20 months ago by mgdrnl10
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Non-standard TCGA FASTQ files
... I am looking at RNA-seq data from TCGA and noticed that some nucleotides are replaced by '.' in the FASTQ files. So far, I only encountered this coding in FASTA files that were repeat-masked. Can this encoding potentially cause any mappers or other down-stream software to fail on such files, or shou ...
fastq tcga rna-seq written 4.0 years ago by Daniel Gerlach30 • updated 3.8 years ago by Biostar ♦♦ 20
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Increased duplication rates on chromosome 21
... Hello, We are performing paired-end 50bp un-stranded RNA-seq experiments on an Illumina HiSeq 2500 system with around 15 million total fragments per sample. While most previous human cell line RNA-seq experiments had duplication rates of around 20-40% pretty much balanced over all chromosomes, I re ...
qc rna-seq written 4.4 years ago by Daniel Gerlach30
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Soft Masked Version Of Hs37D5 Reference
... Hi, I am working with the hs37d5 reference assembly from the 1000 human genome project. For some downstream analysis I would need a FASTA version of the file with repeats soft masked by Repeat Masker as lower case letters. Can I produce such a file or download it already? Cheers, Daniel ...
fasta 1000genomes written 6.8 years ago by Daniel Gerlach30 • updated 6.8 years ago by Pierre Lindenbaum128k

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Popular Question 4.3 years ago, created a question with more than 1,000 views. For Soft Masked Version Of Hs37D5 Reference

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