User: s.vandenhurk

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s.vandenhurk10
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New User
Location:
Netherlands
Last seen:
2 years, 3 months ago
Joined:
2 years, 11 months ago
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s***********@gmail.com

Posts by s.vandenhurk

<prev • 10 results • page 1 of 1 • next >
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Comment: C: DSK error on k-mer lengths up to, say, 160
... yea Im not sure about what I was thinking with trying kmers of bigger then 101. I should map my reads and create contigs and do a kmer analysis on those contigs... thanks for waking me up ...
written 2.6 years ago by s.vandenhurk10
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Comment: C: DSK error on k-mer lengths up to, say, 160
... I am not 100% sure, but I believe all sequences in my file are 101 bp long. the fasta file I want to count is 11GB big. Too bad I can't share the actual file because it contains company property. /Desktop/DSK/dsk-2.0.3-Source/build$ ./dsk -file 'input/location.fasta' -kmer-size 160 [counting kmers ...
written 2.6 years ago by s.vandenhurk10
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Comment: C: DSK error on k-mer lengths up to, say, 160
... It works up to a kmer size of 101 after that the partitioning step get's stuck at 0% with a -1% memory usage. any ideas? ...
written 2.6 years ago by s.vandenhurk10
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Comment: C: DSK error on k-mer lengths up to, say, 160
... It works, thank you so much ...
written 2.6 years ago by s.vandenhurk10
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Comment: C: DSK error on k-mer lengths up to, say, 160
... I will let you know if it works when I get back to work on monday. I don't have access to the network from home. Thanks in advance ...
written 2.6 years ago by s.vandenhurk10
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Comment: C: DSK error on k-mer lengths up to, say, 160
... dsk itself seems to work just fine, that is true. but dsk2ascii does not. it works perfect with 31mers, but it does not with 32+mers ...
written 2.6 years ago by s.vandenhurk10
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DSK error on k-mer lengths up to, say, 160
... I am looking for a k-mer analysis tool that is capable of analysing kmers longer then 31. I thought I hit the jackpot when I read about DKS but so far I have had no luck. Is there any other easy to use tool that is capable of k-mers with a size up to 91+? I have tried the linux package, and got it ...
k-meranalysis dsk written 2.6 years ago by s.vandenhurk10 • updated 2.6 years ago by edrezen690
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automating multiple fastq.gz -> SAM
... Hello Guys, I am interested in automating the combining of multiple fastq.gz files. As you can see in the image below I have already indexed my reference genome with BWA and I have combined the fastq.gz files from my COL strain. Because this Arabidopsis is a test set, I could do it manually. Howeve ...
assembly sequencing written 2.7 years ago by s.vandenhurk10 • updated 2.7 years ago by Pierre Lindenbaum101k
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Comment: C: duplicating features in genbank file with biopython
... is there a way to do this with biopython? and if so, where can I find a guide on how to? I don't mind the fact it wouldn't be a normal GenBank file because I'm the end user of these files in my occasion. ...
written 3.0 years ago by s.vandenhurk10
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duplicating features in genbank file with biopython
... I have got a lot of genbank files with multiple genes in them, some of these genes have a single start and stop position e.g. 1000..1390 and some have multiple start and stop positions e.g. join(1000..1390,1400..1790,1900..2275) I want to duplicate the entire CDS for the genes with multiple start a ...
biopython genbank written 3.0 years ago by s.vandenhurk10 • updated 3.0 years ago by Peter5.6k

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