Tag: sra-toolkit

Index of /debian/pool/main/s/sra-sdk

Name Last modified Size Parent Directory – sra-sdk_2.3.5-2+dfsg-1.debian.tar.xz 2014-07-30 15:22 8.8K sra-sdk_2.3.5-2+dfsg-1.dsc 2014-07-30 15:22 2.1K sra-sdk_2.3.5-2+dfsg.orig.tar.xz 2014-07-30 15:22 2.1M sra-sdk_2.8.1-2+dfsg-2.debian.tar.xz 2017-04-02 00:22 13K sra-sdk_2.8.1-2+dfsg-2.dsc 2017-04-02 00:22 2.1K sra-sdk_2.8.1-2+dfsg.orig.tar.xz 2017-01-24 10:35 2.8M sra-sdk_2.9.3+dfsg-1.debian.tar.xz 2018-10-23 23:07 3.7M sra-sdk_2.9.3+dfsg-1.dsc 2018-10-23 23:07 2.1K sra-sdk_2.9.3+dfsg.orig.tar.xz 2018-10-23 23:07 3.7M sra-sdk_2.10.9+dfsg-2.debian.tar.xz 2021-02-05 03:50 3.7M sra-sdk_2.10.9+dfsg-2.dsc 2021-02-05 03:50…

Continue Reading Index of /debian/pool/main/s/sra-sdk

blastn_vdb Error: Cannot open VDB:

blastn_vdb Error: Cannot open VDB: 0 I’m working locally with sra-toolkit. I have downloaded a sra files, validate it with vdb-validate and when I try to do a search with blastn-dbd the following error occurs Error: Cannot get VDB column: ./SRR7443983.sra.SEQUENCE.ACC_PREFIX Anyone knows how to fix it? Thanks blastn_vdb •…

Continue Reading blastn_vdb Error: Cannot open VDB:

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…

Continue Reading Problems with downloading fastq files from sra-toolkit

getting paired end datasets from SRA

getting paired end datasets from SRA 0 I am searching SRA by keywords like “paired-end”, but the sra-toolkit seems to only download one file (single-end) about 90% of the time. I just want to make sure my commands are all correct: prefetch SRR13310323 fastq-dump -I –split-files –outdir fastq –gzip –skip-technical…

Continue Reading getting paired end datasets from SRA