Hello everybody,
this is my first try to trim Illumina (paired-end) reads on the unix command line.
If i get it correctly, de-multiplexing...
13 results in 0.0029 seconds.
-
Struggling with quality trimming
-
jamespblloyd started a topic How many poor quality bases define a bad read (using fastx or equivalent)?in GeneralHow many poor quality bases define a bad read (using fastx or equivalent)?
I want to know what people who have used fastx or similar have done to define a poor quality read. What do you call a bad base (I was thinking of calling... -
Trimming multiple adapters in a single run
Hi,
I ran the quality control for my fastq reads and found that some adapter seuqences in every sample. I used Fastx_clipper like this:... -
Splitting fastq file by barcodes without producing unmatched.fq file?
G'day Everyone,
I am trying to split six plates of data by the barcodes of 576 indviduals. We are split our data using 'fastx_barcode_splitter.pl',... -
Assembly problems with fastx artefacts filter
Hi All,
I've been using the fastx toolkit to preprocess Illumina HiSeq reads for alignment using shrimp and assembly using Velvet/Oases.... -
Illumina - Paired End Barcode Split + Mip trimmer
Hello,
I've received a data set of old Illumina PE data. (R1, R2, R3).
Paired end files are R1 and R3.
I've split... -
Is the PRINSEQ fastq-format weird?
Hi,
I have been using Prinseq to trim my Illumina data, and the fastq output looks like this:
...Code:@HWI-ST486:386:D1UMHACXX:3:1101:1399:2119
-
Remove the adapter sequence by fastx_clipper in fastq file
I have a really bad pairs of fastq files so I am tried to used fastx toolkit to do quality control.
The main question I have is how do... -
Beginner level trimming question
Hi everyone,
I have some SE small RNA-seq data from which I'd like to trim 3' sequencing adapters. I know of several useful trimming programs,... -
Fastx giving error for Illumina data
Hi,
I'm trying to do some quality scoring/trimming on some Illumina, SE RNAseq data, but keep getting an unusual error message from Fastx.... -
Trimming illumina 1.8 reads
Hi All,
Recently i got data from illumina 1.8.
I am trying to trim bad quality reads, i am using FASTX tool kit for this purpose.... -
FASTX quality plot error
Hi all,
I am using FASTX tool kit to for the quality control. When I run fastq_quality_boxplot_graph.sh script on the quality stats file, I get... -
Fastx collapsed
Hi all,
I was wondering whether there is a way of working in bowtie with the collapsed data from fastx.
I would like to...
