User: Michael Gruenstaeudl

Reputation:
20
Status:
New User
Location:
Berlin, Germany
Website:
http://blogs.fu-berlin...
Last seen:
2 weeks ago
Joined:
2 years, 9 months ago
Email:
m**************@gmail.com

Postdoctoral Researcher at the Freie Universität Berlin

Posts by Michael Gruenstaeudl

<prev • 13 results • page 1 of 2 • next >
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Removing unmatched Ns from query sequence based on alignment
... Assume a contig of draft genome assembly that contains several regions of unknown sequence and length, which are indicated by stretches of 'N'. Further assume the presence of a contig of the same genome region, whose source is a complete and trustworthy genome assembly of the same organism. Finally, ...
genome alignment contig sequence written 14 days ago by Michael Gruenstaeudl20
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Comment: C: Uploading data files to Webin upload area under Linux
... @Juke-34 and @genomax Actually, the issue is an unstable server on the side of ENA. It goes offline intermittently throughout the day. I was unsuccessful ftp'ing to 193.62.192.11 prior to 11:00 CEST, then successful, and since about 14:00 CEST unsuccessful again. AllenKao, in his post above, has co ...
written 7 weeks ago by Michael Gruenstaeudl20
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Comment: C: Uploading data files to Webin upload area under Linux
... Just received an email by ENA that it was a server problem on their side. Seems to be corrected now. ...
written 7 weeks ago by Michael Gruenstaeudl20
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Comment: C: Uploading data files to Webin upload area under Linux
... Interestingly, I am able to connect when I ftp directly to the IP address: ftp 193.62.192.11 Connected to 193.62.192.11. 220 (vsFTPd 2.2.2) Name (193.62.192.11:XXXX): ...
written 7 weeks ago by Michael Gruenstaeudl20
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Comment: C: Uploading data files to Webin upload area under Linux
... @AllenKao Thanks. I used pretty much the same commands in the past. However, I am still unable to even connect to the server, as it hangs at login: $ ftp webin.ebi.ac.uk Connected to hh-webin.ebi.ac.uk. # Hangs here forever. ...
written 7 weeks ago by Michael Gruenstaeudl20
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Comment: C: Uploading data files to Webin upload area under Linux
... @AllenKao Would you mind sharing the precise commands that you are using when ftp'ing to `webin.ebi.ac.uk`? ...
written 7 weeks ago by Michael Gruenstaeudl20
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Uploading data files to Webin upload area under Linux
... The European Nucleotide Archive (ENA) requires certain datasets to be uploaded to the Webin upload area (`webin.ebi.ac.uk`) before they can be submitted via XML files that reference the uploaded file. According to [this doc][1], one can use `lftp` to upload a data file. However, when I try to do th ...
sequence sequencing written 7 weeks ago by Michael Gruenstaeudl20 • updated 7 weeks ago by Juke-341.2k
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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 21 months ago by Michael Gruenstaeudl20
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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 21 months ago by Michael Gruenstaeudl20
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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 ...

Latest awards to Michael Gruenstaeudl

Scholar 21 months ago, created an answer that has been accepted. For A: 2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ

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