R Bioinformatics Reading fastq with Bioconductor

Learn to read fastq files and plot basic quality metrics with R and Bioconductor.

[Minely]

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

[elvinceager]

hello. Is it possible to do bacterial genome assembly either de novo or using a reference genome, directly in R studio? if yes, what are the tools that i may require for this. thank you

[rorykoenen]

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

[Sherry-epzv]

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

[LASCH_B]

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.

[pakman]

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 <- as(quals 'matrix')

[denissedominguezbolanos]

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?

[mahmoodhonarvar]

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