coverageBed using paired-end fastq as input

[cmccabe]

I am new to Illumina data with more experience with Ion Torrent data. Recently, I have some fastq files and before:

CoverageBed using a bam:

 coverageBed -d -a targets.bed -b IonXpress_.bam > IonXpress_output.txt

Now that I have 2 paired-end fastq files:
S5_R1.fastq
S5_R2.fastq

How do I use them with coverageBed? Thank you .

[GenoMax]

And you are back

You seem to have overlooked the step of having to trim/align the fastq files to get an alignment file (BAM) before you can think about coverageBed.

[cmccabe]

I am totally new to Illumina data and admit I did not think of that step. Do you have any recommendations far as what to use or where to begin? Thank you .

[GenoMax]

I am totally new to Illumina data and admit I did not think of that step. Do you have any recommendations far as what to use or where to begin? Thank you .

What kind of data is this? I will suggest starting with BBDuk (to trim data/look for adapters) and then BBMap (to align) but other aligners will work as well.

[cmccabe]

This is Illumina paired-end data from a NextSeq. I will give those to applications a try. Thank you .

[GenoMax]

This is Illumina paired-end data from a NextSeq. I will give those to applications a try. Thank you .

Is it DNAseq, RNASeq, ChIP_seq .. "what-seq" kind of data. BBMap would work for all of those but downstream analysis will be different.

[cmccabe]

It is DNA-seq data. Thank you .

I spent some time reading and learning some programing. Thank you for your helpful posts