Countng reads used in VICUNA

[Gideon Mordecai]

Hi Xiao,

I am using VICUNA to assemble two different viral variants in the same sample and want to roughly know how many reads make up each contig. 

Could you please confirm that it is the contig.align output file that I need to be looking at? All my read names start with '>', so all I did was used a grep command to count each '>'. Is this a valid approach?

 

Thanks very much for your advice,

Gideon

[Xiao Yang]

Hi Gideon,

The short answer is yes. But there's a caveat that if you use alignment software to map reads back to the contig you might get more reads aligned. .algn file only shows you how the contig was constructed but did not provide you with haplotype information. 

best

Xiao

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- Xiao

[Gideon Mordecai]

Great, thanks for your answer.

[Gideon Mordecai]

Hi Xiao,

Using the same method as above to count the number of reads used in the VICUNA alignment, I am finding that there are more reads in the contig.align file than the number of reads that I input to VICUNA for the assemble. Can VICUNA use the same reads twice in different contigs?

Thanks for your help,

Gideon

[Xiao Yang]

Hi Gideon,

To clarify, are you assembly fasta input or fastq input, paired end reads ? If it is paired end reads, I assume you count the input reads by a factor of 2. I dont' remember Vicuna would put a same read in different contigs. 

Xiao 

[Gideon Mordecai]

Hi Xiao, yes they are fasta paired end reads and yes I counted both read 1 and read 2. If that is the case I am not sure what is happening!

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[Xiao Yang]

okie, could you convert it to paired-fastq format, Vicuna has not been tested on paired fasta input and there could be problems with it.