Is it possible to find the positions of mismatches if using mathPDict to align patterns to a sequence of reference ? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Is it possible to find the positions of mismatches if using mathPDict to align patterns to a sequence of reference ?

Hello,

I am using the bioconductor function matchPDict to align quickly a big number of small patterns to the genome. I am authorizing 2-3 mismatches. I get the result with the position for the match of my patterns but I also would like to identify easily the position of the mismatches with the aligments. Is it possible to do that ? Is there a pre-implemented function? I found one for matchPattern but not for matchPDict..

Many thanks!

alignment r sequence

• 2,328 views • link

updated 4.8 years ago by Ram

• written 12.2 years ago by Aurelie MLB

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Aligning very short sequences using bowtie2, I need fine control over how many mismatches are allow…
written 3.0 years ago by Mauro •

Hi, I'm using bowtie2 to align very short sRNA sequences (18-45nt) to reference files. I've been using the very-sensitive-local preset to align to the human …
Best experimental/bioinfo protocol to genotype large insertions?
written 10.9 years ago by Aurelie MLB

Hello, I am trying to find what would be the best way to identify a large insertion (~1kb) in a sequence. Basically, scientists I am …
Ignoring N's on Each Side of the Chromosome
written 11.2 years ago by msmithmailbox •

I'm trying to find the instances of a degenerate DNA sequence (contains N's, R's, K's, etc.) in the human genome. I am using the `matchPattern` …
RNA-seq: how big should be the library?
written 11.3 years ago by Aurelie MLB

Hello, I am wondering how big should be the library for each sample to big enough to detect meaningful differential expression please? Is 15M reads …
Efficient way of calculating the number of mismatches between two sets of sequences please?
written 11.7 years ago by Aurelie MLB

Hello, I am working with R and Bioconductor packages. I have set big sets of sequences such as: ``` A=c("TATTCCTAGGTTCGCCT", "TTCCCGTTGCCCAGTGA"....) # length ~ 500 …
What is in the UCSC/NCBI genomes please?
written 11.9 years ago by Aurelie MLB

Hello, I am looking at the human genome available through Bioconductor packages: NCBI GRCh38 and UCSC.hg19. And I do not get all the different sequence …
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
written 11.9 years ago by Aurelie MLB

Hello, I would like to be able to align around 500 short sequences (~20 nucleotides) to the human genome in a super quick way. I …
GRCh38 Annotation for non coding RNA (e.g. miRNA)
written 12.0 years ago by Aurelie MLB

<p>Hello,</p> <p>Would someone know what tool to use to annotate positions in the Homo Sapiens GRCh38 genome with non coding RNA ids ? I would …
How to link UCSC transcripts ids to protein ids using bioconductor ?
written 12.2 years ago by Aurelie MLB

Hello, I am new to this area so apologies if the answer is obvious. I am currenlty using Bioconductor packages to access the UCSC genome …
Pattern Matching - Biological Compatibility Between Query Reads And Reference Sequence?
written 14.5 years ago by Agatha •

<p>Hi,</p> <p>I was trying to manually align RNA-seq reads to a RNA sequence in R using Biostrings.</p> <p>Considering that my sequences are collapsed </p> <pre><code> …