Question: Mapping soft for de novo assembly
0
gravatar for scheme4193
13 months ago by
scheme419350
scheme419350 wrote:

I am now de novo sequence analysis and now finished de novo assemble and got multi fasta file. I want to make sam file by running mapping software after de novo assembly.

There are several software of mapping, like bowtie2, bwa, hisat2, STAR, tophat2.

I think de novo assembled multi fasta file is different from complete whole genome fasta file. Are they able to mapping even if it is not reference sequence but de novo assembled multi fasta file ? Which supports de novo assembled result ?

Also, if there is recommendation, please tell me !

Thanks

rna-seq mapping assembly • 387 views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 13 months ago by scheme419350
4
gravatar for genomax
13 months ago by
genomax85k
United States
genomax85k wrote:

I think de novo assembled multi fasta file is different from complete whole genome fasta file.

It is different only in the sense that it is not perhaps complete as a model genome reference you would download from NCBI/Ensembl. Otherwise it is just a multi-fasta file and you can create indexes from it to use as a reference with any aligner you want. Depending on how well your assembly worked you would want to make sure that you remove redundancy that may be present in the contigs.

ADD COMMENTlink modified 13 months ago • written 13 months ago by genomax85k
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