Hello,
I'm having trouble extracting assembled reads after using soapaligner.
I mapped my raw reads to my reference genome using soap aligner, how do I then extract the assembly and submit for annotation? I tried converting soap to sam format, then using,
# This is for extracting mapping reads from bam files
samtools view -F4 input.bam > /data/bowtieOutput/mapped.sam
converted sam to bam and bam to fastq, then fastq to fasta -
I need a genebank file to upload sequences to http://rast.nmpdr.org/rast.cgi
Please help!
bgansw
I'm having trouble extracting assembled reads after using soapaligner.
I mapped my raw reads to my reference genome using soap aligner, how do I then extract the assembly and submit for annotation? I tried converting soap to sam format, then using,
# This is for extracting mapping reads from bam files
samtools view -F4 input.bam > /data/bowtieOutput/mapped.sam
converted sam to bam and bam to fastq, then fastq to fasta -
I need a genebank file to upload sequences to http://rast.nmpdr.org/rast.cgi
Please help!
bgansw
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