baoe
commented
9 years ago Hi, Amir,
Sorry for reply late and thank you for the suggestion.
How much extensions AlignGraph can make is mainly dependent on factors like how close the reference genome and the target genome are, and how well the pre-assembly worked. Therefore, in your case, it is possible there is no extension, either because the reference genome is not so similar to the target genome, or because the upstream assemblies are already good enough for the current version of AlignGraph.
We are currently working on improving AlignGraph's performance, so that more extensions can be made with a relatively different reference genome, but this may take some time. We will also support more input file types.
Best, Bao
From: amir feizi [notifications@github.com] Sent: Wednesday, December 31, 2014 11:45 AM To: baoe/AlignGraph Subject: [AlignGraph] empty extendedContigs.fa (#5)
Dear Baoe,
Hi I run AlignGraph on PE reads after de novo assembly of them using velvet. My genome is a fungi and it has not sequenced before I use S.Cerevisiae (yeast) genome as reference genome. First I could not be able to run it because it was giving the PE inconsistency error. It took a while to realize actually AlignGraph needs reads to be as fasta format not fastq, So I converted the reads to fasta format and it run successfully but the problem now is that my extendedcontigns file is empty while the output.stdout file looks like below >
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved
(0) Alignment finished
CHROMOSOME 0: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded
CHROMOSOME 1: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded
CHROMOSOME 2: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded ... CHROMOSOME 16: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded
FINISHED for 4230 seconds (524 seconds for alignment) :-)
So do you have any idea what is the potential problem with that?
Beside I suggest to adjust AlignGraph to run on fastq as many people will also face with the same problem of PE inconstancy error!
Best wishes,
Amir
— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/5.
Dear Baoe,
Hi I run AlignGraph on PE reads after de novo assembly of them using velvet. My genome is a fungi and it has not sequenced before I use S.Cerevisiae (yeast) genome as reference genome. First I could not be able to run it because it was giving the PE inconsistency error. It took a while to realize actually AlignGraph needs reads to be as fasta format not fastq, So I converted the reads to fasta format and it run successfully but the problem now is that my extendedcontigns file is empty while the output.stdout file looks like below >
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved
(0) Alignment finished
CHROMOSOME 0: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded
CHROMOSOME 1: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded
CHROMOSOME 2: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded ... CHROMOSOME 16: (1) chromosome loaded (2) contig alignment loaded (3) read alignment loaded (4) contigs extended (5) contigs scaffolded
FINISHED for 4230 seconds (524 seconds for alignment) :-)
So do you have any idea what is the potential problem with that?
Beside I suggest to adjust AlignGraph to run on fastq as many people will also face with the same problem of PE inconstancy error!
Best wishes,
Amir