Dear all,
We have an alignment file in bam format including three type of reads with different length ( pair-end and mate-pair), we want to do denovo assembly for the novel sequence by using velvet.
We got three fastq files with unmapped reads from the bam file by using picard ViewSam.jar.
How to input these reads to velvet? Since the reads in fastq file are not in proper order, e.g no pair-end relation, can we treat these reads as singletons?
Can we use velvet to handle the three fastq files together?
Many thanks!
We have an alignment file in bam format including three type of reads with different length ( pair-end and mate-pair), we want to do denovo assembly for the novel sequence by using velvet.
We got three fastq files with unmapped reads from the bam file by using picard ViewSam.jar.
How to input these reads to velvet? Since the reads in fastq file are not in proper order, e.g no pair-end relation, can we treat these reads as singletons?
Can we use velvet to handle the three fastq files together?
Many thanks!
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