BLAST unmapped reads from BAM

Hey, I have sequenced a recombinant plasmid and I am trying to characterize the insert sequences that have not aligned to the reference. I have generated a BAM file with the unmapped sequences and now I am trying to BLAST these in various databases to identify the unmapped sequences.

reads unmapped minion dna sequencing bam

• 1,910 views • link

updated 4.1 years ago by Thái Hoàng 0 • | written 4.1 years ago by ummamd 0

What is your question?

• 0 views • link

written 4.1 years ago by JC 1.3K

Assuming you are studying microbes. Maybe you can try de novo assembly and blast the contig to NCBI or other public database.

Velvet assembler source code: https://github.com/dzerbino/velvet

• 0 views • link

written 4.1 years ago by tomas4482 43

0 answers

No answers yet.

More posts like this

Finding Insert in plasmid
written 2.2 years ago by SaltedPork 17

Hi, We sequenced a plasmid on MiSeq, 150bp reads. I have a reference, and an expected sequence of the insert. I want to know at …
Mutect2 for mitochondria variant discovery
written 2.4 years ago by ernestine.kubi 0

I am following the pipeline for mitochondria variant discovery using mutect2. I am currently trying to Align the unmapped BAM file with the reference aligned …
Finding insert sequences using long reads
written 2.6 years ago by bvm 2

I'd like to find insert sequences on a known plasmid using Nanopore long reads. My first idea was to create a reference mapping to the …
Local blast with large query and subject file
written 3.9 years ago by Sowmya Pulapet 7

Hi, I have 2 bam files from which the unmapped sequences have to be extracted and aligned against each other to identify unaligned sequences. The …
Assembly plasmid with tandem repeats of the same insert
written 6.0 years ago by David 24

Hello, I got data from a lab , that is a plasmid that has been recently sequenced with nanopore. The plasmid is roughly 8kb and …
What is the best approach to detect unknown recombinant gene in genome?
written 6.7 years ago by Can Holyavkin 25

We have just sequenced the whole genome of a bacteria. We aim to **detect if any recombinant gene is inserted into the genome**. Inserted gene …
Help with data from rna-seq
written 7.1 years ago by lks50 1

Hi guys, I have some sugar cane fastq files and I need to find the genes contained in my libraries. I've already looked at the …
Obtain sequence of a gene with vector DNA integrated
written 7.6 years ago by kspata 9

Hi, I have 1 plasmid sample sequenced on MiSeq PE150. I have derived the sequence of putative plasmid by de novo assembly (SPADes). The plasmid …
Is there a tool that can identify longer insertions using genome resequencing data?
written 7.9 years ago by JJ 77

Hi all, I am looking for a tool that can identify longer insertions using genome resequencing data (based on Illumina reads). I am searching for …
How To Blast Multiple Contigs To The Reference Database?
written 13.6 years ago by vibhanim.21 4

<p>i have multiple contigs in fasta format after assembling the reads. i also have 33 reference genome sequences. i want to blast the query sample …