check bubbles for /netmount/ip03_home/boisver1/issue-153/Sample_CQDM2-3

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/netmount/ip03_home/boisver1/issue-153/Sample_CQDM2-3

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this task is about testing, not about programming

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The files:

[boisver1@cp2148-mp2 ~]$ ls -lh /home/boisver1/Sample_CQDM2-3/*
-rw-r----- 1 boisver1 corbeil 384M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R1_1.fastq.gz
-rw-r----- 1 boisver1 corbeil 384M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R1_2.fastq.gz
-rw-r----- 1 boisver1 corbeil 385M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R1_3.fastq.gz
-rw-r----- 1 boisver1 corbeil 387M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R1_4.fastq.gz
-rw-r----- 1 boisver1 corbeil 383M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R1_5.fastq.gz
-rw-r----- 1 boisver1 corbeil 102M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R1_6.fastq.gz
-rw-r----- 1 boisver1 corbeil 381M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R2_1.fastq.gz
-rw-r----- 1 boisver1 corbeil 380M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R2_2.fastq.gz
-rw-r----- 1 boisver1 corbeil 382M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R2_3.fastq.gz
-rw-r----- 1 boisver1 corbeil 383M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R2_4.fastq.gz
-rw-r----- 1 boisver1 corbeil 378M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R2_5.fastq.gz
-rw-r----- 1 boisver1 corbeil 101M Dec 22 2011 /home/boisver1/Sample_CQDM2-3/CQDM2-3_Lane5_R2_6.fastq.gz

corbeil group members can read, other can not.

Sample endpoint is located at /home/boisver1/Sample_CQDM2-3

The purpose here is to do 6 assemblies:

-k 21

-k 31

-k 41

-k 51

-k 61

-k 71

Obviously you must compile Ray with MAXKMERLENGTH=71 at least.

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The following options are required too:

-write-kmers -write-seeds

check

Ray --help | less to see what these do.

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see #136 for the definition of a bubble.

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For each job:

1. sort the graph with
   sort -T . kmers.txt > kmers.txt.sort

RayCloudBrowser-client create-map

For the section in Ray Cloud Browser, use the seeds:

cat RaySeeds > Seeds.fasta

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gnuplot figure: /home/boisver1/corbeil_group-lustre03/projects/ray-assembler/tickets/171/3D

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corbeil_group-lustre03 -> /mnt/lustre03/corbeil/corbeil_group

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To find the seeds to check, use SeedLengthDistribution.txt. Take the length (in nucleotides) with the highest frequency. The length most be <= 500 nt too.

Then I suppose you can code a Python script that will fetch any regions with a given length. Alternatively, you can implement a length filter in Ray Cloud Browser.

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@djeef