output all reads in sam file

[fmughal2]

Hello,

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Is there a way to output all reads to the sam file, mapped or unmapped? Currently I only see either unmapped reads or reverse strand mapped reads in the sam?

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Thank you,

-Fizza

[ptlcc]

Hi Fizza

If you use the “-sam” option without an argument it should give both mapped and unmapped.

Which additional arguments did you use.

Best,
Philip

[brbloemen]

Hi Philip,

I encountered a similar issue.

My original fastq file has 701579 (nanopore) reads, and I mapped it to two databases, using a KMA command of the following structure:

kma -i file.fastq.gz -o output_filename -t_db database -tmp /home/brbloemen/workdir \
  -mem_mode -bc 0.7 -bcNano -ID 0.0 -ef -proxi 0.9 -na -nc -1t1 -ca -verbose 2 -t 45 \
  -sam > output_filename.sam

The sample was a defined mock community, and the reads were mapped against two databases. Using samtools view -c to count the alignments:

1. A small, “ground truth” database constructed from the mock community reference sequences

   samtools view -c BBl_pure_GMSspikeI_CB_RAD_GMSspikeIdb.bam

   1. this returns 700804 alignments

2. A large database

   samtools view -c BBl_pure_GMSspikeI_CB_RAD_DTUdb.bam

   1. this returns only 625070 alignments

Interestingly, both resulting samfiles do contain unmapped reads. (each about 1.5% unmapped reads).

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I’m curious as to where this loss of reads could happen.

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Thank you,

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Bram

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[ptlcc]

Hi Bram

It should be fixed in the latest version (1.4.2). The issue only affected unmapped reads, where some where missed.

Best,
Philip