User: K.Nijbroek

gravatar for K.Nijbroek
K.Nijbroek100
Reputation:
100
Status:
New User
Location:
Netherlands
Last seen:
5 years, 1 month ago
Joined:
5 years, 3 months ago
Email:
K*********@utwente.nl

Posts by K.Nijbroek

<prev • 19 results • page 1 of 2 • next >
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Answer: A: How to make Bowtie 2 align the following reads as pairs?
... From the manual:   The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. E.g., if --fr is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length con ...
written 5.2 years ago by K.Nijbroek100
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Comment: C: Paired FASTQ files do not show equal amount of reads
... I did an another additional run for the trimmed FASTQ files and somehow everything went well this time. Now I'm completely flabbergasted.... ...
written 5.2 years ago by K.Nijbroek100
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Comment: C: Paired FASTQ files do not show equal amount of reads
... I will do that. I've also prepared a Bowtie2 command on the raw .FASTQ files (before Trimming), and that works fine. It seems like trimming is doing something wrong... although the number of lines in trimmed files are the same...  ...
written 5.2 years ago by K.Nijbroek100
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Comment: C: Paired FASTQ files do not show equal amount of reads
... Bowtie2: 'Error, fewer reads in file specified with -2 than in file specified with -1'. Both FASTQ files have exact same amount of lines and seqs are not 0 (I require minlen 50). I can't figure out why all other samples prepared with the same processing steps do work, while this one won't... ...
written 5.2 years ago by K.Nijbroek100
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Comment: C: Paired FASTQ files do not show equal amount of reads
... Both FASTQ files have the exact same amount of lines. Seems like Bowtie2 is doing something odd then? ...
written 5.2 years ago by K.Nijbroek100
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Comment: C: Paired FASTQ files do not show equal amount of reads
... I didn't do seperate Trimming, i used Paired-End. Thats why I find it so strange that in this case the FASTQ files show inconsistency, because for other samples it does work.  ...
written 5.2 years ago by K.Nijbroek100
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Paired FASTQ files do not show equal amount of reads
... Hi,   I've got a data sample consisting of two mate-paired FASTQ files. I've applied paired-end Trimmomatic on both these FASTQ files and retrieved a forward_accepted.fq and a reverse_accepted.fq. Now I applied Bowtie2 to align both FASTQ files in forward-reverse order, and it seems like there see ...
fastq paired mate-pairs written 5.2 years ago by K.Nijbroek100 • updated 5.2 years ago by Devon Ryan91k
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Bedtools on Cygwin problem.
... Hi   I'm trying to install the latest release of Bedtools via Cygwin but there's a weird error during process. I know this isn't the best solution, but I do not have an other choice. Perhaps anyone knows how to fix this?   NijbroekK@UTWKS11498 /cygdrive/g/Stage_Enschede/methods/methods_Bedtoolsn ...
bedtools cygwin written 5.2 years ago by K.Nijbroek100
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Bowtie2 align not working
... Hi All, I've downloaded the latest version of Bowtie2 for Windows (bowtie2-2.2.3-mingw-win64.zip), and added the executables directory to PATH. Whenever I try to run something via Bowtie2 I immediately get errors. If I just type 'bowtie2' I already get 'bowtie2-align-s.exe' has stopped working: (ER ...
bowtie2 windows align written 5.2 years ago by K.Nijbroek100 • updated 8 months ago by Biostar ♦♦ 20
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Answer: A: Tophat2 output error
... Problem solved. It wasn't due to the RAM but due to the -p 8. Apparently it only works with -p 1.  ...
written 5.2 years ago by K.Nijbroek100

Latest awards to K.Nijbroek

Scholar 5.2 years ago, created an answer that has been accepted. For A: Tophat2 output error
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: How to make Bowtie 2 align the following reads as pairs?
Scholar 5.2 years ago, created an answer that has been accepted. For A: Tophat2 output error

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