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#Reads Per Contig Information From Assemblies Other Than Velvet

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.

contigs assembly
• 3,351 views • link
updated by Zhilong Jia Zhilong Jia • written by Prakki Rama Prakki Rama

2 answers

Hi Rama,

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

• 131 views • link
updated by Ram Ram • written by Joseph Hughes Joseph Hughes

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?

• 0 views • link
written by Prakki Rama Prakki Rama

fastax_toolkits can get the counts of per reads.

• 106 views • link
written by Zhilong Jia Zhilong Jia

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