Comments (3)
FelixKrueger
commented on August 27, 2024
Talked about it over coffee and decided that we are not going to look into this further.
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jonathanronen
commented on August 27, 2024
Adding one vote to the usefulness of this feature, in case you ever decide to reconsider
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yo54233154
commented on August 27, 2024
Both bowtie and bowtie2 have an --mm option to use memory-mapped I/O for index. bowtie(but not bowtie2) has an additional --shmem option which I think should be similar to that of bwa.
I have tested --mm for standard bowtie2 alignment runs and can confirm that bowtie2 instances against the same index do share memory. This could potentially lower ram requirements for parallel-bismark.
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Related Issues (20)
- Confusion on how coverage is estimated HOT 4
- Low unique alignment % HOT 8
- Analyzing spike in control performance HOT 2
- How to extract methylation levels according to bam file HOT 6
- Correcting low % methylated regions HOT 4
- help combining bismark pipeline with methylated UMIs HOT 8
- Expected unique alignment % HOT 2
- Parent process: Failed to build index HOT 3
- bismark runs to an error when I try to run it using nextflow HOT 4
- Differences in bismark convertion result HOT 1
- Bismark genome preparation issue HOT 3
- Use SRR files with .rar (ziped) format HOT 1
- Dose it necessary to place reads in working directory? HOT 1
- Issue with Perl in filter_non_conversion HOT 4
- bismark for human genome HOT 3
- ambiguous results in .bam file HOT 3
- deduplicate_bismark problem HOT 4
- index of genome faulty or non-existant HOT 5
- Bismark2summary not working for output with hisat2 HOT 6
- directional and nondirectional HOT 6
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