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.

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Steps for trimming aligned peptides using Trimal

I am trimming the aligned peptide sequences and back transleting them to codon using Trimal. Here i am using following cmd's: /mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/trimal-1.4.1/source/trimal -...
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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 ...
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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....
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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.
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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 ...