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There are going to be `N` characters in the input file. I think the proper way to handle these would be NOT to include any kmers containing `N`. As it is now, we throw away the entire _read_ if any …
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when i run :
```
$ ./sc_hla_count_linux -b outs/possorted_genome_bam.bam -c outs/filtered_feature_bc_matrix/barcodes.tsv.gz -o ./outs -d HLA/IPDIMGT/download
```
report it …
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Is there an efficient way to compare large gerbil output files in order to retrieve kmers which are only in one of the two input files?
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I'm having trouble building a gcsa index for the MHC graph I obtained from #363.
```
vg index -g MHC-ref-haps.gcsa -k 11 MHC-ref-haps.vg
```
I've requested over 100G, but the command maxes out aroun…
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I'm trying to run GGCAT on the following dataset: https://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/
I had 5T of free disk space and the following flags: `-k 31 -m 32 -j 8 -s 1`
However, my …
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How fast can we make kmer counting in Rust?
@ctb, are there examples of this from Sourmash or other libraries?
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As I've used spacegraphcats more, I keep returning to the idea that it would be useful to know the percent of k-mers and reads captured by a query or set of queries.
For example, with the Hu SB1 d…
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Hi, I installed your LSHVec from source then tried your hashSeq.py script:
python3 /LSHVec-master/scripts/fastseq/hashSeq.py -i all.fasta --hash lsh -o all.fasta.hash -k 15
2019-12-06 09:58:45,755…
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Hello, I am wondering, does the _in silico_ read normalization script included with Trinity have any capacity to preferentially retain longer reads when choosing which reads to keep or discard? For e…
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Hi Trinity team!
I have a dataset of 168 paired-end fastq files (84 samples) of a total of 428 GB. I'm running Trinity on a server of 64 CPUs, 680 GB of RAM, and 1800 GB of disk space.
```
Tri…