Hello, I am trying to download fastq-files (SRR12273024) with fasterq-dump/fastq-dump from sra-tools. I have tried the --split-files and -s tags however, I only get 1 fastq file.
@SRR12273024.1 SN7001050R:482:HYKG3BCXX:1:1101:1163:2092 length=109 GATGTANAGAACGCGACTTCCACAAACCTGGATTTTTTATGTACAACCCTGACCCNGACCGTTTGCTATATTCCTTTTTCTATGAAATAATGTGAATGATAATAAAACA +SRR12273024.1 SN7001050R:482:HYKG3BCXX:1:1101:1163:2092 length=109 DDDDDI#<<EHIIIHIIIIIIIIIHEHIIIIFHHHIIIIIHHIIIIIIHHIIHHH#<<DGHHIHIHIEHEHHHFHHIIIIIIIH?EEHH@HIIHIIIIFEHDDHHHHHH @SRR12273024.2 SN7001050R:482:HYKG3BCXX:1:1101:1096:2166 length=109 AAGGTACCTGGGTTCAACTAAAGCGCCAGCCTGCTCCACCCAGAGAAGCACACTTTGTGAGAACCAATGGGAAGGAGCCTGAGCTGCTGGAACCTATTCCCTATGAATT +SRR12273024.2 SN7001050R:482:HYKG3BCXX:1:1101:1096:2166 length=109 DDDDDIHIIIHIFHIIIIIIIIIIGIHIIIIIIIIIHIHHHIGHIHIHI?GHHG?GFHHDH@FG<<CHGHIGHHIHHHEHH1FHIIIIIIIGHEHHIIHGHDGHHHHGI @SRR12273024.3 SN7001050R:482:HYKG3BCXX:1:1101:1086:2183 length=109 CAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
I have tried various ways to de-interleave the fastq file including methods outlined in: gist.github.com/nathanhaigh/3521724 and biostars.org/p/19446/ however, none of these methods output fastq files that are compatible with the cell ranger pipeline.
When I try to run cellranger counts on the file, I am given this error:
Log message: The read lengths are incompatible with all the chemistries for Sample SRR12273024 in ./
- read1 median length = 109
- read2 median length = 0
- index1 median length = 0
The minimum read length for different chemistries are: SC5P-R2 - read1: 26, read2: 25, index1: 0 SC5P-PE - read1: 81, read2: 25, index1: 0 SC3Pv1 - read1: 25, read2: 10, index1: 14 SC3Pv2 - read1: 26, read2: 25, index1: 0 SC3Pv3 - read1: 26, read2: 25, index1: 0
We expect that at least 50% of the reads exceed the minimum length.
I've looked into this error and it seems like the dataset is paired-end, which is why I have been trying to split the files using sra-tools to no avail.
Any help is appreciated!