How do I extract read ID after using the Bedtools genome coverage tool?

Question

[SaltedPork]

I have used Bedtools to produce histogram data with:

$ genomeCoverageBed -ibam example.bam -g genome.txt > coverage.txt

I now have the frequency data for my histogram, but now I want to go back and find the read ID's. I've looked through the options on Bedtools and there doesn't seem to be one, any ideas?

[GenoMax]

What exactly do you mean by "find the read IDs"? For a specific interval? If so you could use samtools view with a bed file (Samtools And Region List ). If you truly just need read ID's, then let us know and an addition can be suggested to the solution with samtools.

[SaltedPork]

I have a list of reads which have high frequency/occurances. At the moment, all I can see is what chromosome they are from. I would be choosing the areas of high coverage and wanting to find the ID's for the reads from that region. Thanks for the response.

[GenoMax]

In case you want the full fastq records from the regions you have defined in test.bed you could do

samtools view your_aligned_sorted.bam -L test.bed | awk -F "\t" '{print "@"$1"\n"$10"\n""\+\n"$11}' > your_fastq

If you only need the fastq ID's then

samtools view SRR1972739_sorted.bam -L test.bed | awk -F "\t" '{print "@"$1}' > fastq_ID

[SaltedPork]

Thanks, I now have the list of ID's that I want. Does the new file have ID's that correspond to my BED file, in the same order? Just checking, because I would like to just cut/paste these ID's into my file with the frequencies.

[GenoMax]

They should be in the same order (in terms of sorting) as that was present in your sorted bam file.

[SaltedPork]

Great, Many thanks for your help!