I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans
In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702 ftp and downloaded sra file. Then I need to convert it to fastq file format. For this purpose I've heard that there is a sra-toolkit and within it there is fastq-dump exacutable. However in order to use it, first of all I have to figure out whether my sra file contains paired-end or single-end read data. So my question is that how could I know the type of reads in the dataset (in the first link) ?
Without any information, I used --split_files flag of fastq-dump exacutable and it generated two 14 Gb (both of them are exactly 14.346.367.840 bytes) files and their name are SRR1741330_1.fastq and SRR1741330_2.fastq Does it mean my dataset is paired end ?
As an another question (different but related with part 1). In the SRR1741330_1.fastq file, at some lines, sequences contains different characters such as CCCFFFFFGFHHHGJJJJI#1?FEIGGI... Before looking into these files, I have thought that these sequence lines should only contain the letters of A,G,T and C . What are these F,H,J,I,#,? etc..
My questions might be trivial and unmeaningful but since I'm a totally new person in this area, I could not understand them.
I wonder one more thing, since its related with previous part of my question I asked it here instead of creating new question. After I generate fastq file with dump_fastq executable, all the sequences are length of 50. Does it because of parameters of the dump_fastq executable or its related with original sra file? In other words, could I increase this length?