User: mgdrnl

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mgdrnl10
Reputation:
10
Status:
New User
Location:
Barcelona
Website:
https://github.com/mac...
Last seen:
2 months, 2 weeks ago
Joined:
3 years, 10 months ago
Email:
m*****@gmail.com

Bioinformatician in Institut Hospital del Mar d'Investigacions Mèdiques IMIM

Posts by mgdrnl

<prev • 6 results • page 1 of 1 • next >
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Many 35nt reads with N bases in R1(paired-end) when sequencing with Illumina NextSeq
... Dear All We recently had a Quality Control issue when sequencing RNAseq with polyA capture in Illumina NextSeq. The reads were paired-end (2x75bp) and we found a proportion between 6%-9% of 35nt length reads with all N bases. It is also surprising that those reads all belong to the R1 reads of the ...
illumina rna-seq qualitycontrol written 22 months ago by mgdrnl10 • updated 17 months ago by Biostar ♦♦ 20
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There is any package for sst-RMA normalization in R?
... Dear all I am working in a microarray core facility and we realized that the “Signal Space Transformation” (SST-RMA) normalization method, implemented in the Expression Console software, improves the fold-change of the arrays (higher range of fold change) when compared to conventional normalization ...
rma affymetrix expression console microarray written 2.2 years ago by mgdrnl10
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Comment: C: Submit High-Throughput data to GEO. Problems with FTP connection
... Thanks! I will definitely try ArrayExpress next time. ...
written 2.3 years ago by mgdrnl10
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Comment: C: Submit High-Throughput data to GEO. Problems with FTP connection
... Thank you very much for the recommendation! the truth is I didn't know about SRA. Unfortunately the journal I am submitting the paper asks me to deposit the data (raw data, fastq files) to GEO or ArrayExpress. I will try with ArrayExpress next time, as someone above said it is better.. unless the jo ...
written 2.3 years ago by mgdrnl10
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Submit High-Throughput data to GEO. Problems with FTP connection
... I open this question because I didn't find much information about this topic so far. I am trying to upload data from a RNA-seq project to GEO (387,5GB) with UNIX command line and I am getting the error: Lost data connection to remote host after 1xxxxxxxx bytes had been sent: Broken pipe. The ...
geo ftp next-gen written 2.3 years ago by mgdrnl10 • updated 2.3 years ago by Arup Ghosh2.7k
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Comment: A: Why does submitting high-throughput sequence data to GEO from an Amazon EC2 inst
... Thank you very much for opening the question and for the bash script! I had the same problem when uploading RNA-seq data to GEO. The connection broke several times and it was hard to submit all the fastq files. However, with your script it is working fine for the moment and I am not getting the er ...
written 2.3 years ago by mgdrnl10

Latest awards to mgdrnl

Popular Question 22 months ago, created a question with more than 1,000 views. For There is any package for sst-RMA normalization in R?
Popular Question 22 months ago, created a question with more than 1,000 views. For Submit High-Throughput data to GEO. Problems with FTP connection
Autobiographer 2.3 years ago, has more than 80 characters in the information field of the user's profile.

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