I have sequences from illumina HiSeq 2000. I'll show you the sequence data that I have a bacteria.
fernando@InvDllo04[Lactobacillus] grep -c "^@" *.fq
FCHCTVLADXX_L1_wHAIPI016080-93_1.fq:1106031
FCHCTVLADXX_L1_wHAIPI016080-93_2.fq:1106031
FCHCTVLADXX_L2_wHAIPI016080-93_1.fq:1088418
FCHCTVLADXX_L2_wHAIPI016080-93_2.fq:1088418
As you can see, I have four files with 1106031, 1106031, 1088418, 1088418 sequences. I'm trying to perform an assembly with Velvet. but I am very confused because I do not know how to use these files. I was reading in some blogs and they say it is necessary to use a script from Velvet (shuffleSequences_fastq.pl), i.e.
1) shuffleSequences_fastq.pl FCHCTVLADXX_L1_wHAIPI016081-94_1.fq FCHCTVLADXX_L1_wHAIPI016081-94_2.fq FCHCTVLADXX_L1_wHAIPI016081-94_shuffled.fq
2) shuffleSequences_fastq.pl FCHCTVLADXX_L2_wHAIPI016081-94_1.fq FCHCTVLADXX_L2_wHAIPI016081-94_2.fq FCHCTVLADXX_L2_wHAIPI016081-94_shuffled.fq
3) velveth auto 31,45,2 -fastq -shortPaired1 FCHCTVLADXX_L1_wHAIPI016081-94_shuffled.fq -fastq -shortPaired2 FCHCTVLADXX_L2_wHAIPI016081-94_shuffled.fq
4) velvetg auto_31 -exp_cov auto
I do not know if I'm doing the right thing using the shuffled scritp or if I should just use the option "-separate" and run Velvet as follows:
velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa
where:
-separate: Read 2 separate files for paired reads
-short -shortPaired
-short2 -shortPaired2
And the run "velvetg"...
My confusion here is because I have apparently two files "left.fa" and two "rigth.fa" instead of one as in the previous example.
I'd like you to tell me how to run Velvet
Thank you very much.
fernando@InvDllo04[Lactobacillus] grep -c "^@" *.fq
FCHCTVLADXX_L1_wHAIPI016080-93_1.fq:1106031
FCHCTVLADXX_L1_wHAIPI016080-93_2.fq:1106031
FCHCTVLADXX_L2_wHAIPI016080-93_1.fq:1088418
FCHCTVLADXX_L2_wHAIPI016080-93_2.fq:1088418
As you can see, I have four files with 1106031, 1106031, 1088418, 1088418 sequences. I'm trying to perform an assembly with Velvet. but I am very confused because I do not know how to use these files. I was reading in some blogs and they say it is necessary to use a script from Velvet (shuffleSequences_fastq.pl), i.e.
1) shuffleSequences_fastq.pl FCHCTVLADXX_L1_wHAIPI016081-94_1.fq FCHCTVLADXX_L1_wHAIPI016081-94_2.fq FCHCTVLADXX_L1_wHAIPI016081-94_shuffled.fq
2) shuffleSequences_fastq.pl FCHCTVLADXX_L2_wHAIPI016081-94_1.fq FCHCTVLADXX_L2_wHAIPI016081-94_2.fq FCHCTVLADXX_L2_wHAIPI016081-94_shuffled.fq
3) velveth auto 31,45,2 -fastq -shortPaired1 FCHCTVLADXX_L1_wHAIPI016081-94_shuffled.fq -fastq -shortPaired2 FCHCTVLADXX_L2_wHAIPI016081-94_shuffled.fq
4) velvetg auto_31 -exp_cov auto
I do not know if I'm doing the right thing using the shuffled scritp or if I should just use the option "-separate" and run Velvet as follows:
velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa
where:
-separate: Read 2 separate files for paired reads
-short -shortPaired
-short2 -shortPaired2
And the run "velvetg"...
My confusion here is because I have apparently two files "left.fa" and two "rigth.fa" instead of one as in the previous example.
I'd like you to tell me how to run Velvet
Thank you very much.
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