Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
CRAM is reference based compression so may or may not be of interest for you. http://www.ebi.ac.uk/ena/about/cram_toolkit/
-
-
Hi all, I can't figure out how to specify loseless compression using cramTools (ie retain all quality score info), can someone help me out? In NGCs paper they state a few flags which seem to be discontinued in 1.0. Presumably I specify using --lossy-quality-score-spec but I can't figure out how to set it to 'any/all'. I appreciate any help/ideas on this. Also if I am missing the point and the compression inherently removes quality scores I apologise in advance, I am n00 to the area=PLast edited by bruce01; 01-11-2013, 02:55 AM.
Comment
-
Hi,
I'm in the same situation as Bruce. I want to compress keeping the base call qualities but can't figure out how...
Just did a naïf try:Code:--lossy-quality-score-spec all
Code:Exception in thread "main" java.lang.RuntimeException: Uknown read or base category: a at net.sf.cram.lossy.QualityScorePreservation.parseSinglePolicy(QualityScorePreservation.java:138)
Thanks!
Pablo.
Comment
-
Hi Pablo,
found it on the archives of cram mailing list, the call includes: -L m999 (-L flag is your --lossy-quality-score-spec above). All reads are retained, but you lose column 12+ ('info'). This isn't an issue for me, and the compressed cram file for a 1GB bam is 600MB which is pretty good!
Comment
-
I just noticed this thread, rather late.
There is CRAM from EBI, which has long term support and handles random access. It's the most direct competitor to BAM I would guess.
Alternatives are Goby (similar ratios, but even slower from my experience), Quip (faster encoding, great compression ratio, but no(?) random access) and SamComp1/2 (faster encoding, great compression ratio, no random access, and doesn't really implement the full SAM spec - more of a fastq compressor). Finally on that topic there are tools like quip again, fqzcomp and fastqz for compression of FASTQ data. [All 3 of these were SequenceSqueeze competition entries.]
Comment
-
But as I saw in one of the presentations, it seems CRAM does a lossy conversion from BAM, and introduces false positive and false negatives ? Is CRAM mature now to do a lossless compression from FASTQ and BAM files with random access such as BAM files give ?
Comment
Latest Articles
Collapse
-
by seqadmin
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...-
Channel: Articles
06-06-2024, 07:15 AM -
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 06-07-2024, 06:58 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
06-07-2024, 06:58 AM
|
||
Started by seqadmin, 06-06-2024, 08:18 AM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
06-06-2024, 08:18 AM
|
||
Started by seqadmin, 06-06-2024, 08:04 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
06-06-2024, 08:04 AM
|
||
Started by seqadmin, 06-03-2024, 06:55 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
06-03-2024, 06:55 AM
|
Comment