Fastq_Screen Does Not Detect Any Of The Contaminants
I am running fastq_screen to pick up the contaminants from my fastq file.
The program runs successfully but finds no match. I have used the same data with FastQC and it finds some of the comtaminants in the same data.
Can anyone advise why fastq_screen can not find a match?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
rnaSPAdes running out of memory: oom error
written by ha2606 •
-
Merging fastq files
written by william.mcentegart •
-
Bimodal GC content
written by Folder40g
-
fastq_quality_filter: input file (-) has unknown file format (not FASTA or FASTQ)
written by 4galaxy77
-
Many overrepresented sequences in RNA-seq data. Should them be trimmed out?
written by dgtiezzi •
-
Running a large number of fastq files through FastQC and other downstream analysis programmes for R…
written by sangita_b
-
How To Get Gistic Or Rae Copy Number Variance Data Files For Copy Number Variance From Either Tcga …
written by RoyC •
-
How To Check The Concordance Of Genotypes In Duplicate Samples In Bed And Ped Formats (Produced Via…
written by snp_cook12 •
-
Fastqc Over-Represented Sequences Are Adapters ?
written by sckinta
-
How To Use Cutadapt Effectively
written by roll
what kind of contaminants are you looking for? Which databases do you have specified in your .conf file for the application?
I am looking for the adapters/trimmers. I have the contaminant file from FastQC which I converted into fasta format and indexed it using bowtie. That is my in my .conf file.
You'll need to share the command line you typed, and your config file, before we can help you.