Hello,
I have a Miseq Barcode library run that I am trying to use idemp to demultiplex using the I1.fastq index file from the instrument....
14 results in 0.0030 seconds.
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Miseq Index file Mismatch
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Bowtie2: a specific use where the parameters are not respected
Hello everyone,
I'm writing this post because I observed a strange behavior with bowtie2. And I suspect this behavior to affect mostly alignments... -
Aligning Reads with Overhangs on the Ends (Edges) of Reference Contigs or Scaffolds
Hi all!
Does anyone know any option in any software that could say:
"In the case a read aligns to the beginning or end...Last edited by Fatih; 12-01-2016, 04:29 AM. -
Filtering bowtie2 output sam file by mismatch number
Hi
I got a sam file output from bowtie2 by choosing option -N (setting number of mismatches allowed in a seed alignment during multis alignment)... -
Single position mismatch agglomerate after alignment
Hello folks,
After downloading and realigning the reads of the ChIP-seq sample GSM721212 with bwa, I get a quite strange mismatch profile... -
Bam Output Mismatch By Contig
I've been looking for something that extracts the %mismatch by contig from a .bam file. (Not unlike the left navigation panel in Tablet does automatically.)...Last edited by crkessen; 06-05-2013, 01:45 PM. -
BWA change mismatch penalty between N-mismatch and base-mismatch
Dear all
I am trying to use BWA with different penalty score between N mismatch and a base mismatch [ACTG]. Is there any software option that fits... -
Mask x number of bases WITHIN sequence prior to alignment
Hi all,
As you may see from the picture I have this QC from all R2 reads of my Paired End sequenced samples. Due to a technical error during... -
Filtering raw sequence - mismatch with Ns
I have Illumina reads which I have barcoded prior to adding the Illumina adaptors. I now need to sort the raw reads into separate files before mapping.... -
Set ssaha2 parameter for mismatch
I want to align 454 reads against a transcriptome reference using sssaha2. Tolerance are set to five mismatchs for each alignment. Which parameter can... -
mapping mismatches with Rsamtools, or best approach
Hi,
Given a bam file, I wish to identify the mismatches (state and position, ie. A->T at 21) between my mapped reads and my reference.... -
BWA: mismatch setting (Does '-n 3' allow up to three mismathces?)
Hi everyone,
I used BWA to map my paired end sequencing data. The length of read is 74bp. I would like to allow up to 3 mismatches in... -
Use of custom schema in corona-lite pipeline
I would like to fix "specific" positions for mismatches in reads before mapping. For example : for a 35bp long read : 2 random mismatches in... -
maq with no mismatches
Hello,
Is it possible to run maq to allow no mismatches in the alignment? I tried using -n but that doesn't seem to allow 0 as a value....
