17 results in 0.0037 seconds.
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ErikTheNord started a topic error/mismatch rate threshold for long-read alignment with GMAP or minimap2in Generalerror/mismatch rate threshold for long-read alignment with GMAP or minimap2
Hello all -- my bioinformatics experience is mostly with mapping Illumina reads (to mammalian transcriptomes) using STAR. But lately my group is starting... -
Which parameter is reflecting the maximum number of mismatches when using bwa aln
I have seen some discussions about this but still cannot confirm the answer.
My question is that if I want to allow 3 mismatches when using bwa... -
Barcode splitter
Hello,
I am trying to use fastx barcode splitter, but I do not understand if with the option "partial matching " I can allow indel inside... -
de novo contigs don't match mapped reads
Hi all,
I'm confused about the results I get when I map the reads back to the contigs from Abyss. There are a number of contigs where the... -
Finding mismatches between two sequences using R
Hi,
I am new to R programming. I have two fasta files namely WT and MT that contains 3 protein sequences which is given below
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GSNAP: (too many?) mismatches in -N mode
I've just tried running GSNAP version 2014-12-29 to predict novel splice junctions using -N. My input files are paired-end fast files, 75t.
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Demultiplexing MiSeq Runs with Miseq Reporter
By default, MiSeq Reporter allows up to 1 mismatch when demultiplexing an indexed MiSeq run. Can I force the software to perform exact matches while demultiplexing... -
bowtie number of mismatches and multiple aligned reads
Hi
Should the --no-1mm-upfront parameter be used with bowtie2 to allow exactly 1 vs 2 mismatches? If so how to use it?
Should 1... -
Snp
Why every mismatch is not SNP(single nucleotide polymorphism) in query genome sequence w.r.t reference genome?
If u know the... -
Tool for counting mismatches in hundreds of files?
Hello, I need to align 2 sequences in hundreds of files and then write a list with the count of the mismatches in each file.
I thought... -
how many mismatches does BWA-MEM tolerate during mapping
Hi,
Recently I am trying to use BWA-MEM to do alignment on PE-90 reads, I have some questiones list as following;
1,how... -
BWA with no mismatches - n=0?
Hello,
We have a sample containing several bacterial species and we want to uniquely map RNA-seq reads to the genomes of each of our organisms... -
Bowtie 2 parameters
Hi All,
I am using bowtie 2 to align some illumina sample data on an influenza genome which has less than 14k nt. The samples have more... -
Retrieving mismatch details from tophat
Hi, all,
Summary: How can I see the details of the mismatch locations for tophat alignments?
Details:
In... -
Allowed maximum number of differences in BWA
The paper says the following:
Given a read of length m, BWA only tolerates a hit with at most k differences (mismatches or gaps), where...
