I was testing out converting fastq to uCRAM for some Illumina reads, but seem to have an issue going fastq->uCRAM->fastq that doesn't happen when going fastq->uBAM->fastq or even fastq->uCRAM->uBAM->fastq.
samtools import -i -1 reads_1.fq.gz -2 reads_2.fq.gz -o reads.cram
samtools fastq -i --index-format i8i8 -1 reads_roundtrip_1.fq.gz -2 reads_roundtrip_2.fq.gz reads.cram
If I roundtrip through uBAM (or uCRAM->uBAM), the original and roundtrip read looks like
@A01050:184:HCK2CDSXY:3:1101:2510:1141 1:N:0:ATGAGTCG+AACTAGGC
TGCTTCCACTCGAGATGAATGCCTGTCTCCCCGGGTGCGTCTGGAATGCAACCCCGAGATCCCTGTCGCCCCTGGAGAGGAACAGTGGCTTCTGGACACAAGCCTAGATGAGGTCTATTGGCCCTGCAGTCACTCGAGAGCAATCCCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFF
But when I try and go directly back from uCRAM->fastq, the barcode tag is wrong ("0" instead of "ATGAGTCG+AACTAGGC")
@A01050:184:HCK2CDSXY:3:1101:2510:1141 1:N:0:0
TGCTTCCACTCGAGATGAATGCCTGTCTCCCCGGGTGCGTCTGGAATGCAACCCCGAGATCCCTGTCGCCCCTGGAGAGGAACAGTGGCTTCTGGACACAAGCCTAGATGAGGTCTATTGGCCCTGCAGTCACTCGAGAGCAATCCCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFF
This was on
samtools 1.21-17-g9e91173-dirty
Using htslib 1.21-15-g1d2e493b-dirty
htscodecs=1.6.0-5-g5a2627e
but also occurs on the bioconda v1.21 version.
I was testing out converting fastq to uCRAM for some Illumina reads, but seem to have an issue going fastq->uCRAM->fastq that doesn't happen when going fastq->uBAM->fastq or even fastq->uCRAM->uBAM->fastq.
If I roundtrip through uBAM (or uCRAM->uBAM), the original and roundtrip read looks like
But when I try and go directly back from uCRAM->fastq, the barcode tag is wrong ("0" instead of "ATGAGTCG+AACTAGGC")
This was on
but also occurs on the bioconda v1.21 version.