Problems with downloading fastq files from sra-toolkit

Problems with downloading fastq files from sra-toolkit

1

I have been trying to download the fastq files of a single cell RNA experiment from SRX8632237 with the following SRA runs :

  • SRR12108143
  • SRR12108144
  • SRR12108145
  • SRR12108146

The runs show that it has 3 reads per spot (link). However, I am unable to download the three fastq files separately using sra-tookit (2.10.7). I always get one file.

I have tried multiple combination of fasterq-dump and fastq-dump to download the samples and used the options --split-files, --split-spot, --split-e, --split-3, --concatenate reads, --include-technical, --skip-technical, with prefetch, without prefetch and none of the combinations splits the files according to the reads.

Could someone please help me resolve this problem and let me know where I might be going wrong?

Thanks in advance!!


sra-toolkit


10X-Genomics


NCBI


single-cell

• 38 views

It works AOK for me. Just using --split-files works for most cases:

fastq-dump --split-files SRR12108143

head -20 SRR12108143_1.fastq
@SRR12108143.1 NS500717:249:HT5TNBGX5:1:11101:21539:1043 length=8
TTCAGGTG
+SRR12108143.1 NS500717:249:HT5TNBGX5:1:11101:21539:1043 length=8
AAA/AEEE
@SRR12108143.2 NS500717:249:HT5TNBGX5:1:11101:24889:1044 length=8
TTCAGGTG
+SRR12108143.2 NS500717:249:HT5TNBGX5:1:11101:24889:1044 length=8
AAAAAEE/
@SRR12108143.3 NS500717:249:HT5TNBGX5:1:11101:8341:1044 length=8
TTCAGGTG
+SRR12108143.3 NS500717:249:HT5TNBGX5:1:11101:8341:1044 length=8
/A/AAE/E
@SRR12108143.4 NS500717:249:HT5TNBGX5:1:11101:17829:1044 length=8
TTCAGGTG
+SRR12108143.4 NS500717:249:HT5TNBGX5:1:11101:17829:1044 length=8
/6/6A/66
@SRR12108143.5 NS500717:249:HT5TNBGX5:1:11101:4268:1044 length=8
TTCAGGTG
+SRR12108143.5 NS500717:249:HT5TNBGX5:1:11101:4268:1044 length=8
6AA6AEEE

head -20 SRR12108143_2.fastq
@SRR12108143.1 NS500717:249:HT5TNBGX5:1:11101:21539:1043 length=26
GGAGCNAAGTATTGGACTGCACGAGG
+SRR12108143.1 NS500717:249:HT5TNBGX5:1:11101:21539:1043 length=26
AAAAA#EEEEEEEEEEEEEEEEEEEE
@SRR12108143.2 NS500717:249:HT5TNBGX5:1:11101:24889:1044 length=26
CGGACNCCAAACCTACACCCACGCGC
+SRR12108143.2 NS500717:249:HT5TNBGX5:1:11101:24889:1044 length=26
A6AAA#/EEEE/EEEEEA/EAA/EEE
@SRR12108143.3 NS500717:249:HT5TNBGX5:1:11101:8341:1044 length=26
ACCTTNACACGTAAGGAAGCTTTTGC
+SRR12108143.3 NS500717:249:HT5TNBGX5:1:11101:8341:1044 length=26
6AAAA#EE/EEEEE/EE6EEEEEEEE
@SRR12108143.4 NS500717:249:HT5TNBGX5:1:11101:17829:1044 length=26
GCTGTNCCTCGTCTTCTTCACTAAAG
+SRR12108143.4 NS500717:249:HT5TNBGX5:1:11101:17829:1044 length=26
A6AAA#E6EE/EEEEEE/AEAEE//E
@SRR12108143.5 NS500717:249:HT5TNBGX5:1:11101:4268:1044 length=26
ACCGTNACACAAGCCCTTACGTTGTG
+SRR12108143.5 NS500717:249:HT5TNBGX5:1:11101:4268:1044 length=26
/AAAA#EEEEAEEEEEEAEEEEEEEE

head -200 SRR12108143_3.fastq | tail -20
@SRR12108143.46 NS500717:249:HT5TNBGX5:1:11101:25528:1060 length=49
NGAGCCAAAGCCCCCAGTGTTTGTATTTTGACGCCAAGCTTCACTTTAA
+SRR12108143.46 NS500717:249:HT5TNBGX5:1:11101:25528:1060 length=49
#A//AEE/EEEA6EE<EE///<A/<E/AEEA//<<//EAE<//6E/EEE
@SRR12108143.47 NS500717:249:HT5TNBGX5:1:11101:22932:1060 length=49
NATCACTACTCTAGGAAGGAAGGAAAACCTGACAACCTGAGCAAGAAGG
+SRR12108143.47 NS500717:249:HT5TNBGX5:1:11101:22932:1060 length=49
#A/AA/EE///</E//E/<////E///E/EA</<//<E/6<<//EE/A<
@SRR12108143.48 NS500717:249:HT5TNBGX5:1:11101:15378:1060 length=49
NAAAACATGATTGTCGAGGAGTGTGGCTGCTCCTAGAGTCGCGAGGTAC
+SRR12108143.48 NS500717:249:HT5TNBGX5:1:11101:15378:1060 length=49
#//AAA/AEAEA/A/EEE//A//AE<AAAAE<AA/E/EE</6///66/A
@SRR12108143.49 NS500717:249:HT5TNBGX5:1:11101:20756:1060 length=49
NGATCAACATTACTTATTGTTTGAATACTACGACAACTAAAATTTCACT
+SRR12108143.49 NS500717:249:HT5TNBGX5:1:11101:20756:1060 length=49
#/AAAEE6//EAE<<AA<////////<//E6/<////AAAE6//A/<</
@SRR12108143.50 NS500717:249:HT5TNBGX5:1:11101:11867:1061 length=49
NTATAAAGATGTTTAAAAAAGTCAGTTGCTTTTTTCGCGTAATGTGAAT
+SRR12108143.50 NS500717:249:HT5TNBGX5:1:11101:11867:1061 length=49
#A/AA/E/EE////E/EE/A//EEEEEEE/<<//A/E/AEE6A/AEEA<


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