how to creat reads mapping graph

[pony2001mx]

Dear All,

How to generate the graph visualizing the mapping of reads on a gene? Below I show a graph in a published paper. Could you recommend to me what softwares can do this job. Actually what I do is not genome-wide scale, is to locate reads to a small locus, and then to visualize this mapping.

Thanks greatly!!

[paolo.kunder]

You can just load your bam file in IGV or SeqMonk or IGB and zoom to your specific region

http://bioviz.org/igb/

https://www.broadinstitute.org/igv/

https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

[pony2001mx]

THANKS, Paolo.kunder, how to generate bam file? If I don't perform very large scale assembling, what tools can I use to create bam file? THANKS!

[paolo.kunder]

Have you mapped your reads against a reference genome??

A BAM file (.bam) is the binary version of a SAM file. A SAM file (.sam) is a
tab-delimited text file that contains sequence alignment data

[ak352]

1.) If you want to map your reads to a reference, check out the tools here and choose the appropriate one.

2.) The read-mapping should always give you a SAM or BAM file as output. If you have either one, you can convert between them using samtools.

3.) As Paolo said, the BAM file can then be used by IGV or other tools for visualisation.

[pony2001mx]

THANKS, ak352.