User: edrezen

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edrezen720
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France
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Posts by edrezen

<prev • 76 results • page 2 of 8 • next >
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Comment: C: What tools you use or know for PacBio Long Read error correction?
... Just for information, the hyperlink for LoRDEC in your post (http://www.atgc-montpellier.fr/lordec/) does not seem to work (404 not found). ...
written 5.0 years ago by edrezen720
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Answer: A: minia kmer limit
... Hello, By default, this version 2.0.3 of minia supports kmer sizes up to 127. If you want to use greater kmer size, you need to compile it with a maximum value of your choice; you can do the following (the k4 value should be a multiple of 32) ``` wget "http://gatb-tools.gforge.inria.fr/versions/s ...
written 5.1 years ago by edrezen720 • updated 12 months ago by RamRS30k
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Answer: A: comparing two genomes
... Hello, The blastn command actually executes the megablast algorithm by default. The megablast algorithm is very fast but finds fewer results than the blastn algorithm. If you want to execute the blastn algorithm, you should try the following : blastn -task blastn -db db_file -query input_file.tx ...
written 5.1 years ago by edrezen720
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Comment: C: process substitution input
... Here I talk about the dbgh5 command itself (DiscoSNP uses this command to build a de Bruijn graph from the input reads). For memo, the `-in` parameter of dbgh5 can be one of the following: 1. a fasta file; ex: reads.fa 2. a gzipped fasta file; ex: reads.fa.gz 3. a list of fasta files (gzipped or n ...
written 5.2 years ago by edrezen720 • updated 12 months ago by RamRS30k
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Comment: A: process substitution input
... Hello, I think it's not possible to do so because the dbgh5 command actually reads the input file several times: 1. Computing statistics about part of the input file (statistics about minimizers distribution) 2. Reading the kmers from the input file and dispatching them in partitions (according to ...
written 5.2 years ago by edrezen720 • updated 12 months ago by RamRS30k
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Answer: A: Kmer and rev-comp in separate nodes
... Ok, my answer was focused more on the de Bruijn graph than on the kmers abundances. Strange enough, we never considered for GATB the possibility to count kmers as they appeared in input sequences, maybe because we were interested in creating de Bruijn graphs where a node holds both a kmer and its r ...
written 5.2 years ago by edrezen720
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Answer: A: Kmer and rev-comp in separate nodes
... Hello, No, GATB does not allow to have two distinct nodes for a kmer and its reverse complement. ...
written 5.2 years ago by edrezen720
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Comment: C: DiscoSNP++ 2.2.0 Segmentation Fault
... 157 GB should correspond to the directory where the dbgh5 command is launched, in your case : /home/cmb-02/sn1/tkitapci/software/DiscoSNP++-2.2.0-Source/build/ext/gatb-core/bin so there is something odd if you checked that this directory has 10 TB of free space. By default, all temporary files w ...
written 5.2 years ago by edrezen720
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Comment: C: DiscoSNP++ 2.2.0 Segmentation Fault
... Hi Rayan, you're right, it was misleading to talk about DSK, I meant the de Bruijn graph building in general. Normally, the size of the DSK contribution in the final HDF5 file is about 16*nbSolidKmers bytes, so in this case the DSK contribution is about 32 GB, less than the 157 GB available disk sp ...
written 5.2 years ago by edrezen720
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Comment: C: DiscoSNP++ 2.2.0 Segmentation Fault
... I tried myself to force the "max_file_nb" value to 32768 and test on some reads but I got no problem. By the way, do you get exactly the same error if you relaunch your command ? ...
written 5.2 years ago by edrezen720

Latest awards to edrezen

Scholar 13 months ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 2.3 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Popular Question 2.6 years ago, created a question with more than 1,000 views. For New version of the GATB library
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Life cycle of a fastq file
Popular Question 3.0 years ago, created a question with more than 1,000 views. For All-in-one NCBI / EBI / Amazon BLAST workstation
Popular Question 4.5 years ago, created a question with more than 1,000 views. For KLAST, a Blast-like tool for fast sequence similarity searches: free academic version
Commentator 4.6 years ago, created a comment with at least 3 up-votes. For C: hash function for DNA sequences
Scholar 5.4 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 5.6 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 5.6 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Supporter 5.7 years ago, voted at least 25 times.
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
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Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Scholar 6.3 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models

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