Dear group,
I have data from an experimen where 4 biological replicates were sequenced (exon-capture).
The experiment is paired-end method.
Gerald output the sequences for 4 lanes as S-1-sequence.txt,---, S-4-sequence.txt.
I will be using BWA and samtools:
1. Solexa sequece -> sanger FASTQ
2. Sanger FASTQ + BWA -> .sai
3. .sai -> .sam
4. sam -> bam
5. sort bam -> snp/indel calls.
Since i have to use sampe, there are few questions:
1. sampe requires, s1.fq, s2.fq, s1.sai, s2.sai - how do I get these two s1.fq and s2.fq.
2. What are insert sizes option in sampe.
3. I have only one sequence file per lane. How does paired end data looks .
4. Do i have to seperate one sequence file from one lane to s1.fq and s2. fq
Please help me.
thank you.
I have data from an experimen where 4 biological replicates were sequenced (exon-capture).
The experiment is paired-end method.
Gerald output the sequences for 4 lanes as S-1-sequence.txt,---, S-4-sequence.txt.
I will be using BWA and samtools:
1. Solexa sequece -> sanger FASTQ
2. Sanger FASTQ + BWA -> .sai
3. .sai -> .sam
4. sam -> bam
5. sort bam -> snp/indel calls.
Since i have to use sampe, there are few questions:
1. sampe requires, s1.fq, s2.fq, s1.sai, s2.sai - how do I get these two s1.fq and s2.fq.
2. What are insert sizes option in sampe.
3. I have only one sequence file per lane. How does paired end data looks .
4. Do i have to seperate one sequence file from one lane to s1.fq and s2. fq
Please help me.
thank you.
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