Fastq
I need to make a python program for
- Sequencing depth
- Read count
- Q30 percentage
- Average read quality score From a fastq file I did most but i keep getting stuck.. anyone help??
fastq
basic
• 833 views
•
link
updated
by
Mensur Dlakic
•
written
by
민채 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How do I calculate read depth of sequencing?
written by Madde •I am a co-author on a paper, and they are asking me for read depth of sequencing of a bacterial organism. They did 2x150bp Illumina …
-
Dramatically worse R2 sequencing read quality compared with R1 quality for 10x scRNA-seq library - …
written by Devin •Hi all, I am in desperate need of some help with a sequencing experiment and would be very grateful for any of your thoughts. I …
-
Trimmomatic; How to get only q20 < q < q30 reads
written by SSK •Hi! At first, I used trimmomatic with an average quality score per 4 bp of >= 30, and made bam file by using bwa mem. …
-
Custom filteration of fastq file
written by vivekr •I need to do custom filtration in fastq file as follows: 1. Remove reads having at most 2 bases under quality score 20. 2. Remove …
-
Which mapping tool takes read quality score into account
written by Chen SunRead quality score is an important information, if the quality score for certain position is very low, then the nucleotide at that position might be …
-
Sequenced reads have high average Q30 but all the sequences are the same. How is this possible?
written by from the mountainsMy HiSeq run yielded an average quality score of over Q35, with >90% of the bases being >Q30. Yet, when I analyze these reads, I …
-
FastQC stuck at 95% read sequences forever
written by bxiaHi, I just encounter another problem, after I convert SRA file to FASTQ, and use fastQC to check the quality, The program stuck at 95% …
-
Understanding Trimmomatic Sliding Window Approach
written by nikelle.petrilloHello all, I am performing de novo transcriptome assembly. I have used Trimmomatic to quality filter my reads. I used the argument: SLIDINGWINDOW:4:30 Can someone …
-
Query about HiSeq 2500 System
written by HGHi Everyone, Can anyone share some practical experience about Bacterial Whole genome Sequencing on HiSeq 2500 System (2x250bp Chemistry) I would like to know mainly …
-
Fastq Quality Check
written by toshnam<p>Hi all,</p> <p>I'm trying to check sequencing quality of FASTQ file from HiSeq2000. I used fastx_quality_stats script of FASTX-Toolkit (Version 0.0.13) for it. However I've …
Why not use already existing programs such as FastQC? You should also post a reproducible example of where you are getting stuck if you want people to help.
Let me tell you how your request reads to me. You want to reinvent the wheel, and want to do it using only plastic components. There are wheels out there, and there may be better ones, but you want to do it using plastic. You are not telling us why this is necessary. You are not providing any proof of your own effort to get this done. So you want someone to reinvent the wheel for you for unknown reasons and with no effort on your part. Did I get that right?
I think your chances of getting someone to help are slim no matter what. At least there would be a chance if you provided a compelling reason for doing this and showed a significant effort, where maybe someone can help push you over the hump.