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15 votes
5 answers
2k views

Good / recommended way to archive fastq and bam files?

We have a lot of Illumina sequenced exome data. Currently we are using spring for its great lossless compression, but we are looking if there is anything better (and most preferably opensource) which ...
Karthik Nair's user avatar
1 vote
2 answers
376 views

How to convert CRAM file with 10x data in three fastq files

10x Genomics data are stored in three FASTQ files, besides the standard R1 and R2 reads, there is also a I1 file with some metadata. Sometimes however they are shipped in a single bam/cram file (e.g. ...
2 votes
3 answers
559 views

Accessing .bam/.cram files from AWS S3?

What's the best/easiest way for accessing .bam/.cram files from S3? I have .bam/.bai .cram/.crai and .bed + .gff files that I want to make available easily to others so they can browse in IGV and ...
719016's user avatar
  • 2,324
11 votes
1 answer
344 views

Can I create a CRAM file with a relative reference path?

I’m trying to create a CRAM file that stores its path to the FASTA reference as a relative path, rather than an absolute path, so that I can move the files around. Unfortunately I can’t get this to ...
Konrad Rudolph's user avatar
14 votes
1 answer
957 views

Why would someone use a CRAM instead of a BAM?

I had this question from a graduate student yesterday, and I was stuck. What should I say? Why use a CRAM instead of a BAM? When is it a good idea to use a CRAM instead of a BAM? When is it a bad ...
EB2127's user avatar
  • 1,423