Hello,
I have a problem with the conversion of fastq file to sra. Only available tool I found is called fastq-load from sra toolkit but I dont get the usage from very brief help which represents whole documentation.
I manage to create run.xml and experiment.xml files but I am also a little bit confused which version of xml fastq-load uses, because there are several of them by EBI (http://www.ebi.ac.uk/ena/submit/preparing-xmls). The files that I currently have do not make fastq-load stop, but there are some other errors so they have to be incorrect:
I would really appriciate any sort of help. Thanks in advance. Please do not advice to submit data to SRA libraries - I want hem only locally so far.
Now I am trying the conversion on fastq file originally downloaded as sra (but I want other files in sra - http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1366930). It contains single end 51 b long reads.
Thanks in advance.
I have a problem with the conversion of fastq file to sra. Only available tool I found is called fastq-load from sra toolkit but I dont get the usage from very brief help which represents whole documentation.
I manage to create run.xml and experiment.xml files but I am also a little bit confused which version of xml fastq-load uses, because there are several of them by EBI (http://www.ebi.ac.uk/ena/submit/preparing-xmls). The files that I currently have do not make fastq-load stop, but there are some other errors so they have to be incorrect:
Code:
alena@boxer:/media/Data/Alena/Data/Julie/rawdata$ fastq-load -r run.xsd -e experiment.xsd -o /media/Data/Alena/Data/Julie/rawdata/ -i /media/Data/Alena/Data/Julie/rawdata/ -v 2015-08-05T17:12:03 fastq-load.2.5.2 warn: file="JMJD3_1.fastq" offset="0" 2015-08-05T17:12:03 fastq-load.2.5.2 warn: quality_scoring_system attribute not set for this file, using Phred as default 2015-08-05T17:12:03 fastq-load.2.5.2 err: path incorrect while creating manager within database module - failed to create table with schema NCBI:SRA:Illumina:tbl:phred:v2 2015-08-05T17:12:03 fastq-load.2.5.2 err: path incorrect while creating manager within database module - accession="" status="failure" 2015-08-05T17:12:03 fastq-load.2.5.2 err: path incorrect while creating manager within database module - load failed: path incorrect
Now I am trying the conversion on fastq file originally downloaded as sra (but I want other files in sra - http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1366930). It contains single end 51 b long reads.
Code:
head JMJD3_1.fastq @SRR1232291.1 HISEQ:60:D1VB2ACXX:7:1101:1684:1983 length=51 CAGGCCCAGAACCACCTCAAGTCGGCCTCCCCANNNNCAGCTGCAGCCTCC +SRR1232291.1 HISEQ:60:D1VB2ACXX:7:1101:1684:1983 length=51 B@BDDFFFFHHHGJJJJJJJHHIIHGIIJJJIJ####000BCGEHCDGHIJ @SRR1232291.2 HISEQ:60:D1VB2ACXX:7:1101:2385:1976 length=51 ACCCNGGAGGTGGAGCTTGCAGTGAACCAAGATNNNNGTGCCACTTCACTC +SRR1232291.2 HISEQ:60:D1VB2ACXX:7:1101:2385:1976 length=51 ???D#2ABDD:ADEEEIIIIEIEEIEEIEIDID####00?DDEIIIEEIIE @SRR1232291.3 HISEQ:60:D1VB2ACXX:7:1101:2562:1981 length=51 GCGCAATCCCTGGGAGCCAGGATGAGCAGCACCNNNNAGCCGTAGGAGCCC
Comment