reads with no quality score

[ziphra]

Hello,

I noticed some reads had no quality score in my bam files generated with lra. (278604 out of 2.7 millions reads).

I wonder why ?

My bam were generated as follow:

zcat $FASTQ | lra align -ONT -t 24 $REF - -p s | samtools sort -@ 14 -o $BAM
samtools index $BAM -@ 34

Thank you!

[mchaisso]

This sounds like a bug. I'll tr and look into this.

[ziphra]

Hello,

Thank you for your response.

I thought for a moment that the reads with no quality scores were only unmapped reads, but it appears I have all types of reads that lack quality sequence.

Here is a table summarising the number of reads I have for each category of reads and their flag:

Sam Flag	All reads	With quality score	Without quality score
0	1 465 876	1 416 309	49 567
2048	276 887	270 331	6 556
2064	174 337	170 082	4 255
16	993 862	956 031	37 831
4	604 014	440 413	163 601

I have 240k reads with no quality score from the bam I used there, out of 2,6 million sequences.

Many thanks in advance!

[WenyuLiang]

This sounds like a bug. I'll tr and look into this.

Hello! Thanks for this wonderful tool, but this bug still exists.