User: Michael Gruenstaeudl

Reputation:
10
Status:
New User
Location:
Berlin, Germany
Website:
http://blogs.fu-berlin...
Last seen:
8 months ago
Joined:
1 year, 8 months ago
Email:
m**************@gmail.com

Postdoctoral Researcher at the Freie Universität Berlin

Posts by Michael Gruenstaeudl

<prev • 6 results • page 1 of 1 • next >
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Answer: A: 2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ
... Turns out that the Python package [ngsutils][1] can do said transformation. python2 /path_to_github/ngsutils/ngsutils/fastq/fromfasta.py file.csfasta file_QV.qual > file.fastq [1]: https://github.com/ngsutils/ngsutils ...
written 8 months ago by Michael Gruenstaeudl10
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2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ
... The C++ coded tool `solid2fastq` in the package [BFAST][1] was able to merge native SOLiD files (i.e., `file.csfasta` and `file_QV.qual`) into a colorspace-encoded *FastQ* format. Specifically, the sequences remained in colorspace, but the quality values were re-formatted to abide to *FastQ* specifi ...
fastq solid conversion written 8 months ago by Michael Gruenstaeudl10
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Running samtools mpileup on BAM that contains colorspace
... I have some SOLiD data from way back and aligned the reads in colorspace to reference genome *my_ref* via `MosaikAligner`. The output of said assembler is a `BAM` file that, if sorted, indexed (both via `samtools`) and eventually converted to `SAM`, exhibits information in colorspace. user$ sam ...
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Commandline alternatives for generating EMBL flat files from NEXUS alignments
... One of the default tools to generate EMBL flat files from NEXUS-formatted multiple sequence alignments is the "old workhorse" Sequin. I also understand that the genome browser Artemis has a similar functionality, and Artemis is the recommended method for the conversion nex2embl. Neither tool has com ...
python embl sequence nexus submission written 14 months ago by Michael Gruenstaeudl10
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Code design of DNA alignment degapping when annotations
... This is a question regarding a more efficient code design: Assume three aligned DNA sequences (strings; seq1, seq2 and seq3) that represent two genes (gene1 and gene2). Start and stop positions of these genes are known relative to the aligned DNA sequences. # Input alignment = {"seq1":"ATGCATGC", ...
sequence alignment written 15 months ago by Michael Gruenstaeudl10
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Answer: A: Converting Ab1 Trace Files Into Scf Trace Files
... The converter supplied in the package Staden works perfectly for such tasks. For example, from within your folder containing the .ab1 files, you can run: for i in $(ls *.ab1); do convert_trace -out_format scf < $i > ${i%.ab1*}.scf; done ...
written 20 months ago by Michael Gruenstaeudl10

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