What's wrong with the following fastq file? Why don't I see any nucleotides?
@SRR867022.1 s0205_20091123_4_Boot2_1_2_22_F3 length=50
T33001001113133.110110230.0021001100032033.3.133111
+SRR867022.1 s0205_20091123_4_Boot2_1_2_22_F3 length=50
!(+*.)
I would suggest you to contact your sequencing facility to get more details and any fix if possible.
The reads are probably encoded in color space:
- https://en.wikipedia.org/wiki/FASTQ_format#Color_space
- http://gensoft.pasteur.fr/docs/cutadapt/1.12/colorspace.html
Cheers
Nothing is wrong with the dataset. The dataset you have was sequenced on ABI SOLID (https://www.ebi.ac.uk/ena/data/view/SRR867022) which used colorspace as mentioned by Nuno A Fonseca .
Since in 2020 Solid is almost a dead sequencing technology and rearly used. And thus we don't have good enough software for Solid fastq format.
For these sequence reads, its not possible to directly transform the colour codes to bases.
Therefore, you need to
1) contact Sequencing facility to provide the required software which can be used to read the solid fastq reads and transform it into fasta format which can be used for the assembly purpose. Easy way.
OR
2) get the denovo2 assembly tool from solidsoftware website (A dead website). But the tool still exist in the GitHub with some modifications from unofficial sources. Previously this tool was using Velvet but this unofficial version includes MUMmer. You need to know basic CLI operations to be able to use it and fulfill the task. Sort of convoluted way.
Not sure what abouts for the modified software's performance.
I could not find the solidsoftware website which might possibility to download the software.
Following is the link to the new tool, you may also need to find a way to run this software. As I could not find any manual.
https://github.com/MWSchmid/ABI_SOLiD_software_mirror/blob/master/README.md
I also attached the manual of the original denovo2 in case you get access to the software.
3) you may find out a way to trim the solid fastq sequences based on quality. After this step, you can simply remove the qual values and use the colour space sequence in velvet for the assembly.
-/Posted from Android
There are plenty of open source conversion tools to deal with that data. BFAST aligner has a script to convert those files, GALAXY has a "solid2fastq" tool and there are various publicly available instances of GALAXY running at university hosted sites. It is also available as a standalone PYTHON script available in BitBucket. If you're pulling color space data from NCBI's SRA, it has tools to convert them as well. There are other PERL, PYTHON scripts to do it as well in several other open source packages (MAQ for one).
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