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Search: Posts Made By: reliscu
Forum: Bioinformatics 10-13-2021, 12:30 PM
Replies: 693
Views: 249,557
Posted By reliscu
All "N" reads in paired reads not being filtered if other read is "good"

Version 38.94

This thread details the "bug":
https://www.biostars.org/p/9493307/#9493339
Forum: Bioinformatics 10-13-2021, 09:57 AM
Replies: 0
Views: 595
Posted By reliscu
BBDuk quality filtering not producing expected result

I'm trying to trim/filter low quality reads from paired-end exome-seq data, using BBDuk.

I used the command:

```
for ea in $files;
do
R1="$ea"
R2=$(echo $R1 | sed "s/R1/R2/")...
Forum: Bioinformatics 05-16-2021, 04:46 PM
Replies: 2
Views: 1,167
Posted By reliscu
Thanks for your quick response! Very helpful.

Thanks for your quick response! Very helpful.
Forum: Bioinformatics 05-16-2021, 03:52 PM
Replies: 2
Views: 1,167
Posted By reliscu
Can trimmomatic be used on paired interleaved fastq files?

Apologies for the simple question, but I can't seem to find a straight forward answer searching online.

I created interleaved fastq files for each of my libraries, and was going to proceed with...
Forum: Bioinformatics 05-16-2021, 01:53 PM
Replies: 1
Views: 1,111
Posted By reliscu
Can all R1 and R2 files be combined prior to interleaving?

My questions is whether it's okay to to combine multiple R1 and R2 fastq files (i.e. resulting in two files: R1.fastq and R2.fastq), and then use those as input for interleaving to produce a single...
Forum: Bioinformatics 05-08-2021, 01:26 PM
Replies: 3
Views: 1,199
Posted By reliscu
Thank you for your response! To clarify, I...

Thank you for your response!

To clarify, I could do something like this:

Combine all R1 fastq files from L1 >> R1_L1.fastq
Combine all R2 fastq files from L1 >> R2_L1.fastq
>> Then trim these...
Forum: Bioinformatics 05-08-2021, 11:59 AM
Replies: 3
Views: 1,199
Posted By reliscu
Combining fastq files from paired-end WES prior to trimming and alignment

Hi there!

I've tried to find answers to questions that apply to my scenario, but I'm still unsure about the kosher way to approach this. I should say, I'm very new to this side of bioinformatics....
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