R Bioinformatics Reading fastq with Bioconductor

Learn to read fastq files and plot basic quality metrics with R and Bioconductor.
Code: github.com/rsh249/bio331_2021...
Install the ShortRead library: bioconductor.org/packages/rel...
More on Phred scores: en.wikipedia.org/wiki/Phred_q...

[@rorykoenen5027]

Thanks a lot for this great instruction video. Very helpful to me (R proficient, but RNAseq beginner).

[@Minely182]

Thanks a lot. I hope you will submit more videos, please.

[@LASCH_B10]

Hello i'm new to sequencing, first of all thank you for creating this video, this is very helpful, and complements a course that i'm taking right now. I have some experience using R, so i reproduced your code with my fastq file. However, all of my fragments have 150 bp long, i even added some code lines to actually test this within all the reads (by using table func), thereby quality graph appears to show nothing but it's actually a block cause there's no difference between reads... should i suspect that this is not actual raw data? (I was not in charge of anything prior or during sequencing, so i just received this fastq file, and as far as i know the sequencing service was done outside our lab). I hope you can help to solve my question with your experience.

[@LASCH_B10]

oh just checked literature... this seems bad

[@ReubenSarwal]

Hi Luis! I'm having the same issue. Were you able find a solve for this or a reason as to why this is happening?

[@LASCH_B10]

@@ReubenSarwal hello Reuben, so first of all, illumina paired-end sequencing is mostly set up to produce 150 no short reads. Now as much as great Illumina can be, that won't always happen. So with my previous post, I was seeing a great quality score for all my reads, and it's obvious why I got that output in R. I found the files of the report of the sequencing service in a drive, so effectively this prove to be a case where the providers filtered the reads, and gave us the reads with the greatest quality scores. Hope that can help you in some way. Btw I'm still fresh at this subject, but perhaps we can help ourselves as we learn, so feel free to contact me any other time.

[@Sherry-ep6zv]

The shortread packages cannot successfully installed on the windows...

[@mahmoodhonarvar3520]

> fq = readFastq('SRR13764788.fastq') Error: Input/Output no input files found dirPath: SRR13764788.fastq pattern: character(0)

[@denissedominguezbolanos9373]

How can i convert fasta to fastq? in NCBI the only download option is fasta and when i try to convert fasta to a fastq it dosen't let me due the format. or where can i find/download the sequence of a virus in format .fastaq?

[@robh1305]

You can read fasta with Biostrings from Bioconductor. bioconductor.org/packages/release/bioc/html/Biostrings.html library(Biostrings) fa

[@pakman8680]

My quals file is too big I get the error 'long vector not supported yet' when I try to convert it to matrix. Any work around? numqscores

[@sianhamer3703]

I am having the same error generated, is this something to do with R itself ?

[@robh1305]

That happens with large files. It is possible to read batches of the object and convert the smaller chunks to avoid this. I don't have this demonstrated at the moment.