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
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This is one of the files?
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
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>
3 - use 'Tabular-to-FASTA'
4 - Use the tool "'NGS: QC and manipulation: Combine FASTA and QUAL
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,