#Reads Per Contig Information From Assemblies Other Than Velvet

Question

[Prakki Rama]

Hi all,

Could someone help me guiding how to get number of reads per contig from assemblies other than velvet?

I used mapping using bowtie and tried to get .sam file, but i m confused whether to consider end to end or local option to verify the read information.

Please spare and correct me if am not thinking in correct way.

Answer 1

[Joseph Hughes]

Hi Rama,

I think you will find an answer here for SAM/BAM assemblies generated from bowtie or bwa.

[Prakki Rama]

Thank you for your answer Joseph Hughes. But when i compared the read information file obtained from velvet (through AMOS) and the read information file obtained after mapping with bowtie, sam tools i find they are not the same.

Similarly, when i want to know read information in a contig, while mapping should i consider end to end or local in bowtie parameters?

Or else is there any other better mapping tool?

[Joseph Hughes]

There are loads of methods for mapping, look at this biostars post: What methods do you use for short read mapping? They will all give slightly different results based on the parameters used for alignment.

Answer 2

[Zhilong Jia]

fastax_toolkits can get the counts of per reads.