Questions tagged [genome-index]

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need bam file for pilon

I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file. How do I make a BAM file of the resulting assembled.fasta?
rimo's user avatar
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0 votes
1 answer

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

I am trying to perform a HISAT2 indexing using a GCF_000001405.39_GRCh38.p13_genomic.gtf and ...
Dmitrii Trubetskoy's user avatar
1 vote
1 answer

Why index a sequence file with minimap2?

I have been using minimap2 for a few month now and I just found a script that follows these steps: ...
Paul Endymion's user avatar
2 votes
0 answers

Merging/concatenating index files

I was wondering if any one has had success merging pre-generated reference index files for BWA, bowtie2 from multiple references? For a concrete example I have hg19 and a bunch of viral and ...
Bioathlete's user avatar
  • 2,574
1 vote
1 answer

STAR Indexing Diference for Small and Large Genome File Output

I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file. Genome size is 3GB, here is the file output ...
San's user avatar
  • 23
1 vote
1 answer

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

I am running the following command to index my genome: ...
Biomagician's user avatar
  • 2,459
5 votes
1 answer

Can I index a compressed FASTA file using STAR?

I am using STAR to align RNA-seq reads to a reference genome. Before the alignment, I need to generate an index of the reference genome. I use the following code to generate the index successfully: <...
Biomagician's user avatar
  • 2,459