Hello,
This is one of the files? GSM803805_ZMR3_trimmed.txt.gz
ID = Unique sequences identified
ZMR3_raw = Abundance count (raw value)
ZMR3 = Abundance count (tags per million)
ID ZMR3_raw ZMR3
TCAAGATTGCATGTAGAAGAGGAAA 1 1
AAGATAGAAGTCAAACACGTT 1 1
AAGCAATTCGAAGGTCGT 1 1
CGAACGAAGATCGCTCACGATC 1 1
GACTGTTGTGGATGATTACTCTAG 1 1
GGAGATCGTGGCTAAGACTT 1 1
AAGCTAATGTGAACTCTGA 1 1
TGTGAGCATACCTGTCGGGACTCGTATG 1 1
Yes, you can create a FASTQ file from this. Tools under "Text or FASTA Manipulation" unless noted.
0 - Load the file(s) 1 - 'Add column' starting with 1 and choosing to increment. This assigns a unique identifier. Or add in any other type that you want - tools in this same tool group can help rearrange data. 2 - 'Cut' out the fourth and first column (result: identifier <tab> sequence). 3 - use 'Tabular-to-FASTA' 4 - Use the tool "'NGS: QC and manipulation: Combine FASTA and QUAL into FASTQ'. Do not choose a quality score file. 5 - Double check the datatype is ".fastqsanger" and reassign the "database" as needed. 6 - Optional: extract a workflow (History menu) from the method the first time through, save, and run on subsequent files.
Hopefully this helps,
Jen Galaxy team
On 11/7/13 12:30 AM, Jonathan Glass wrote:
Hi There
Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using both Bowtie 1 and Bowtie 2. Im currently using publicly available data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28755) which is not available in FASTQ format - only the raw sequences with the read count. Is there a way to set the input data for bowtie to raw, as is possible using the terminal? Or is there a way to convert a raw sequence to FASTQ (not sure if this would work, but it might be possible if I assigned accession numbers to each sequence and made all the quality scores identical)?
Thanks very much Jonathan Glass Disclaimer - University of Cape Town This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.
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