kart file in prefetch
to download files from SRA by sra toolkit , there is a tool that named "prefetch". its command contains "kart file". https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch What ia kart file? and its format?
rna-seq
• 14,185 views
•
link
updated
by
Biostar
•
written
by
zh.khodadadi •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Understanding NCBI vs ENA data
written by wes •I want to download PacBio RSII data with [accession number SRR6037732][1] for further analysis. In NCBI, there are both SRA archive files and original format …
-
Downloading authorized data from dbGAP leads to a "looped" message
written by Hussein_95 •Hello everyone, I am trying to download authorized dbGAP data. My PI gave me the .ngc key and the necessary kart file. I used this …
-
Prefetch not working for SRA
written by NewtoBioinfo •Hello, I'm new to bioinformatics. I installed sra-tools through conda on my Mac Terminal. Then tried the prefetch tool to download SRA run data but …
-
Help downloading original data from SRA
written by stefan.grabuschnig •Hi biostars community! I am trying to download the original fastq paired-end read files from three biosamples of a bioproject from SRA. For example: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8581464 …
-
i can't find the SRR sample on NCBI FTP, such as SRR018260
written by zhao03 •I used FTP to search SRR018260 that i want to download, however, SRR018260 sample can't be found. is the website error? or i should download …
-
SRA files bulk downloads
written by S ARHow do i use aspera or wget to download the SRA files in bulk either by RUN/Sample/Experiemts. My SRA ID list contains IDs from Exp …
-
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
written by Wenhu_CaoThis is a brief tutorial about methods of downloading sra, sam and fastq files, mainly focusing on Aspera Connect. ## NCBI-SRA and EBI-ENA databases [SRA: …
-
How to download SRA fastq filese
written by 110300553 •I've generated a csv file with the run info for a bioproject SRA using the command: wget 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&rettype=runinfo&db=sra&term=PRJNA223640' -O - | tee SraRunInfo.csv Which I …
-
Cannot find downloaded files from SRA toolkit (prefetch)
written by Lina FHi all, I would like to download a few datasets from NCBI's SRA resource. I installed the SRA toolkit on a Mac (10.11.6) and tried …
-
Sra-Pileup Question
written by Sergei Lebedev •<p>I'm having trouble extracting a <a href='http://samtools.sourceforge.net/pileup.shtml'>pileup</a> file from an <a href='ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX101/SRX101206/SRR364089/SRR364089.sra'>SRA</a> using <code>sra-pileup</code> command. NCBI <a href='http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sra-pileup'>documentation</a> only covers command line arguments for the …
Kart aka Cart file is mentioned here on the NCBI webpages.
this seems to me like one of this comprehensively documented features of ncbi utilities... While I was trying to understand how the heck such a kart file is supposed to look like this is probably the best advice I got from Sej Modha's comment "in addition to bulk download with cart-file, the prefetch can also run with individual SRA accession, which is often preferred method for program/script directed automatic download. "