Oxford Nanopore sequencing_summary.txt file description

Question

[anastasiia.satyr]

Hello,

I have a problem with understanding of some values in "sequencing_summary.txt" file. Unfortunately, I did not manage to find any description of this file on Nanopore community page.

The file consists of columns:

filename    read_id run_id  batch_id    channel mux start_time  
duration    num_events  passes_filtering    template_start  num_even
ts_template template_duration   sequence_length_template    mean_qsc
ore_template    strand_score_template   median_template mad_template

what do all the lines with "template" mean? Where the basecaller takes the information about this "template"?

Thanks, Anastasiia

Answer 1

[WouterDeCoster]

Once upon a time, there was 2D sequencing, which had a template and a complement (the complementary strand) sequenced after each other. In most library preps now (1D) there is only the template fragment. Note that there is also 1D^2, which is conceptually very similar to 2D but without a covalent link.

So the template is just the read. template_start is the start of the read, mean_qscore_template is the mean qscore of the read, and so on.

[anastasiia.satyr]

Thanks a lot, I've already got it :)

But, the new challenge appeared - I have a problem with SAM/BAM conversion for nanopore data. When I convert SAM file to BAM using samtools, the output BAM file lacks information about mapping (as it is binary file). I decided to use CRAM format, but I cannot find appropriate program for variant calling (I mean, a program which can input the CRAM file).

Maybe you could give me a prompt on how to solve the problem?

[WouterDeCoster]

That's a separate question and doesn't belong in the current thread.

[anastasiia.satyr]

So, maybe you could comment it in original thread?

C: .bam format is not enough for mapped long reads

[WouterDeCoster]

So, maybe you could follow up on Devon's comment there?