Gert Hulselmans
Gert Hulselmans
Preferably run with the same amount of threads as you have CPUs (or with one less to account for some overhead), so in your case with `-t 14` or `-t...
BWA mem2 is optimised for mapping short reads and likely performs very badly on very long reads.
You could also use samtools fixmate with `-m` option to add the MQ tag: ``` bwa-mem2 ... | samtools fixmate -u -m -O bam - - > sample.bam ```
I managed to write a rough prototype that can stream gzipped files. gzip compressed CSV file: - uncompressed size: 4,4GB - compressed size: 1.2 GB Reading first 100000 rows of...
I wrote a Polars IO plugin that will stream the decompression of CSV/TSV files instead of decompressing the whole file in memory first: https://github.com/ghuls/polars_streaming_csv_decompression It should support almost all options...
@dpinol See: https://github.com/pola-rs/polars/issues/18724#issuecomment-2657400855
Try to run with less threads or make sure you have enough memory.
What I did a few years ago, was to to rewrite the tid and mtid fields after using `samtools reheader`. ``` // List of BAM files with BAM files with...
Probably you would see the same variation if you keep the same expression matrix, but just run with different seeds.
I didn't even know this was supported in normal `awk`. In `mawk` the printing does not work like expected (as a for loop over the array does not go necessarily...