![]() |
|
![]() |
||||
Thread | Thread Starter | Forum | Replies | Last Post |
Problem with BWA mapping of Illumina PE short insert size fragments (FFPE material) | LadyGray | Bioinformatics | 2 | 10-22-2012 02:20 AM |
Short fragments removal- Amplicon sequencing | sanju0891 | 454 Pyrosequencing | 7 | 03-29-2012 06:43 AM |
sequencing of short DNA fragments (40-240bp) | volks | SOLiD | 1 | 09-07-2010 06:04 AM |
Short reads fragments of genome... | hicham | Bioinformatics | 2 | 03-24-2010 05:15 AM |
PubMed: Phylogenetic classification of short environmental DNA fragments. | Newsbot! | Literature Watch | 0 | 02-21-2008 06:17 AM |
![]() |
|
Thread Tools |
![]() |
#1 |
Junior Member
Location: Florida Join Date: Apr 2012
Posts: 6
|
![]()
Hello,
I've recently performed Illumina PE (2x75) sequencing of enzymatically-fragmented genomic DNA, where the fragments going into the library prep ranged from 20 to 400 bp. I would like to align these reads to a reference genome to obtain locations and insert sizes, while discarding all reads that are not paired. Based on this workflow, we assume (to use bowtie2 manual terminology and diagrams) that: 1) Mates may 'overlap' each other Code:
Mate 1: GCAGATTATATGAGTCAGCTACGATATTGTT Mate 2: TGTTTGGGGTGACACATTACGCGTCTTTGAC Reference: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGCGTCTTTGAC Code:
Mate 1: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGC Mate 2: TGTTTGGGGTGACACATTACGC Reference: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGCGTCTTTGAC Mate 1: CAGCTACGATATTGTTTGGGGTGACACATTACGC Mate 2: CTACGATATTGTTTGGGGTGAC Reference: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGCGTCTTTGAC Code:
Mate 1: GTCAGCTACGATATTGTTTGGGGTGACACATTACGC Mate 2: TATGAGTCAGCTACGATATTGTTTGGGGTGACACAT Reference: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGCGTCTTTGAC After clipping 3' adapters and low-quality ends, and filtering reads of low quality, I've attempted to align these reads with bowtie2: Code:
bowtie2 --dovetail --no-mixed --nodiscordant --no-unal -x reference -1 mates1.fastq -2 mates2.fastq -S aligned.sam It seems that this population of ~75-bp insert sizes is an alignment artifact. What can I do to test or resolve this? I cannot find another alignment program that explicitly states they can handle mates that dovetail or contain each other. |
![]() |
![]() |
![]() |
Thread Tools | |
|
|