Questions tagged [trimming]
To cut from the end. Trimming is often done on raw Illumina reads to discard low-quality bases or adapter sequences. Questions related to trimming algorithms, when, how to trim, trimming software.
6
questions with no upvoted or accepted answers
1
vote
0
answers
59
views
Can files with different R1 and R2 lengths be trusted?
I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples?
Also, I had to do a trimming over the R2 at 220(...
- 11
1
vote
0
answers
76
views
Steps for trimming aligned peptides using Trimal
I am trimming the aligned peptide sequences and back translating them to codon using Trimal.
Here i am using following cmd's:
...
1
vote
0
answers
167
views
Why is cutadapt discarding some paired end reads?
So, I am using cutadapt to remove two primers from some paired end reads.
I have 2 files for each sample, i.e. sample_R1.fastq and sample_R2.fastq.
I have primer_1 and primer_2 and both of them can be ...
- 320
1
vote
0
answers
166
views
FastQC and Trimmomatic in Galaxy?
I am independently working on data retrieved SRA database, paired-end data as separate inputs.
The proceedure I followed is,
After running FastQC using Galaxy, the majority of the modules have failed....
1
vote
0
answers
243
views
Calculating the trimming parameter when constructing an additive phylogeny
How do you calculate the trimming parameter when constructing an additive phylogeny?
I think it has a relationship with the length of the shortest hanging edge, but I can't figure out how this works.
- 11
0
votes
0
answers
76
views
FastqCleaner in R, not recognizing paired-end fastq file?
I've recently downloaded the FastqCLeaner to process paired-end fastq files locally using R (4.0.3). I'm having trouble with the shiny app. It is not uploading my second fastq file, and is repeated ...