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7 votes
Accepted

Why index a sequence file with minimap2?

If you don't provide an index, minimap2 will just generate the index on the fly (so, yes, it's done without specifying it). As such the mapping step will take longer. However, index generation is ...
DavyCats's user avatar
  • 507
5 votes
Accepted

Can I index a compressed FASTA file using STAR?

I can think of two possible workarounds. The simplest would be to try using zcat instead of gunzip -c, in case that works. ...
terdon's user avatar
  • 10.2k
2 votes

need bam file for pilon

Run a short-read mapper. For example: bwa index assembled.fasta bwa mem -pt16 assembled.fasta read1.fq.gz read2.fq.gz \ | samtools sort -m4G -@4 -o align.bam -
user172818's user avatar
  • 6,535
1 vote
Accepted

How can I bypass 'out of memory' problem using a HISAT2 for human genome indexing?

You haven't allocated the requisite 160GB of RAM required. Or rather, you allocated 160GB of memory, which is what you were told to do, but they most likely meant 160GiB. Computers use binary, not ...
Jose Fernando Lopez Fernandez's user avatar
1 vote
Accepted

STAR Indexing Diference for Small and Large Genome File Output

You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of ...
Devon Ryan's user avatar
  • 19.6k
1 vote
Accepted

Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?

A std::bad_alloc error tends to mean that you've run out of memory. It's not unusual for head nodes to be fairly limited in capacity, so presumably that's the issue....
Devon Ryan's user avatar
  • 19.6k

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