Comments (4)
The offset in the read id is referring to the two new fasta references generated by SURVIVOR.
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Is there a straightforward way to translate the positions in the read identifiers to those in the original FASTA (i.e. hg19)? I am looking to do this in order to judge alignment accuracy. The alternative would be to look at the distance between mates, which (as far as I can tell) should be equal for both sets of positions if the alignments are accurate. This could still produce false positives, however.
Again, thanks for your help and prompt replies.
from lrsim.
I suggest you to use -d 1 -2 0 -3 0 -4 0 -5 0 -6 0 -7 0 to enable haplotype simulation mode and disable simulating unbalanced structural variants.
from lrsim.
Alright, that seems like the best solution -- thanks.
from lrsim.
Related Issues (20)
- LongRanger crashes HOT 1
- LRSIM hangs during manifest generation step HOT 4
- LRSIM does not filter out duplicate reads with different barcodes HOT 1
- R1 R2 reads count inconsistent
- Problem with installing LRSIM HOT 4
- Small test-set sequence
- Can't locte Math/Random.pm HOT 1
- Barcode issue in few-molecules case HOT 2
- time HOT 13
- Increased read depth flanking N-stetches in reference HOT 1
- Few SNPs generated using two haplotype sequence HOT 1
- non overlapping region HOT 27
- Complile fails HOT 1
- LRSIM phase4 problem HOT 1
- Extension to BGI stLFR HOT 1
- Using LRSIM with LongRanger: Extremely high rate of incorrect barcodes observed (99.90 %) HOT 13
- SURVIVOR step not progressing HOT 1
- LRSIM crashes and reports "not defined chr1_182578874_182579@chr1" HOT 1
- Ran out of barcodes HOT 3
- 0 readpairs per molecule
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