I have questions about running "Velvet".
What I want to do is de novo assembly with short read sequence.
Data Description:
- I have fastq files generated from Illumina.
- These are paired end reads.
- There are four lengths of DNA.
- There are two lanes. (The same samples are loaded on two different lanes.)
- One fastq file contains one end of particular length of DNA.
e.g. lane1_2-4kb_R1.fastq was generaged from lane1, containing right end of DNA of 2-4kb length
- 16 fastq files in total (R1 and R2 are paired ends.)
______________________________
_________Lane1______Lane2_____
2-4kb........R1...R2........R1...R2
5-7kb........R1...R2........R1...R2
8-10kb.......R1...R2........R1...R2
11kb..........R1...R2........R1...R2
______________________________
My Questions:
- The first thing that I need to consider is to shuffle the paired data files into one merged file; (lane1_2-4kb_R1.fq and lane1_2-4kb_R2.fq into merged.fq)
Q1. However, do I have to distinguish two different lanes? If not, can I just put all the fq files into one command?
Q2. Do you think the command below makes sense?
Thank you in advance.
What I want to do is de novo assembly with short read sequence.
Data Description:
- I have fastq files generated from Illumina.
- These are paired end reads.
- There are four lengths of DNA.
- There are two lanes. (The same samples are loaded on two different lanes.)
- One fastq file contains one end of particular length of DNA.
e.g. lane1_2-4kb_R1.fastq was generaged from lane1, containing right end of DNA of 2-4kb length
- 16 fastq files in total (R1 and R2 are paired ends.)
______________________________
_________Lane1______Lane2_____
2-4kb........R1...R2........R1...R2
5-7kb........R1...R2........R1...R2
8-10kb.......R1...R2........R1...R2
11kb..........R1...R2........R1...R2
______________________________
My Questions:
- The first thing that I need to consider is to shuffle the paired data files into one merged file; (lane1_2-4kb_R1.fq and lane1_2-4kb_R2.fq into merged.fq)
Q1. However, do I have to distinguish two different lanes? If not, can I just put all the fq files into one command?
Q2. Do you think the command below makes sense?
velveth \
Dir 31 \
-shortPaired2 -separate -fastq 02_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 02_L8_R1.fq 02_L8_R2.fq \
-shortPaired2 -separate -fastq 05_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 05_L8_R1.fq 02_L8_R2.fq \
-shortPaired2 -separate -fastq 08_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 08_L8_R1.fq 02_L8_R2.fq \
-shortPaired2 -separate -fastq 11_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 11_L8_R1.fq 02_L8_R2.fq
Dir 31 \
-shortPaired2 -separate -fastq 02_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 02_L8_R1.fq 02_L8_R2.fq \
-shortPaired2 -separate -fastq 05_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 05_L8_R1.fq 02_L8_R2.fq \
-shortPaired2 -separate -fastq 08_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 08_L8_R1.fq 02_L8_R2.fq \
-shortPaired2 -separate -fastq 11_L7_R1.fq 02_L7_R2.fq \
-shortPaired2 -separate -fastq 11_L8_R1.fq 02_L8_R2.fq
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