SRA-tools fasterq-dump and cellranger issues

1

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#<<[email protected]
@SRR12273024.2 SN7001050R:482:HYKG3BCXX:1:1101:1096:2166 length=109
AAGGTACCTGGGTTCAACTAAAGCGCCAGCCTGCTCCACCCAGAGAAGCACACTTTGTGAGAACCAATGGGAAGGAGCCTGAGCTGCTGGAACCTATTCCCTATGAATT
+SRR12273024.2 SN7001050R:482:HYKG3BCXX:1:1101:1096:2166 length=109 [email protected]<<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!


cellranger

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