Hi all,
First post in Seqawnsers so bare with me.
I've recently completed a set of transcriptome assemblies using SOAP Denovo trans. The output is looking good, except I would prefer to limit all contigs output by SOAP to be greater than a set no. of nucleotides. (300 e.g.)
I ran SOAP using ASM_FLAG set to 1 to limit it to a contig assembly.
As it stands the output has thousands of short 'contigs' of 18 nt long. Which makes me think that these are simply the shortest raw reads I've input into SOAP that did not get assembled into a longer contig.
I thought setting the -L flag ( minContigLen) would limit contig size but that didn't work.
Could anyone help me out ? Any suggestions will be much appreciated.
Lahcen
First post in Seqawnsers so bare with me.
I've recently completed a set of transcriptome assemblies using SOAP Denovo trans. The output is looking good, except I would prefer to limit all contigs output by SOAP to be greater than a set no. of nucleotides. (300 e.g.)
I ran SOAP using ASM_FLAG set to 1 to limit it to a contig assembly.
As it stands the output has thousands of short 'contigs' of 18 nt long. Which makes me think that these are simply the shortest raw reads I've input into SOAP that did not get assembled into a longer contig.
I thought setting the -L flag ( minContigLen) would limit contig size but that didn't work.
Could anyone help me out ? Any suggestions will be much appreciated.
Lahcen