Can you guide me on how could take an input fastq file, read the length from read and then feed it into the findtail's command?
I have suggested concerns about documentation and program defaults to my prof and asked him to switch to cutadapt instead of using findtail that has no documentation. But he refuses so I have no option but to proceed with what he wants.
I want the user to input a RNA-seq data fastq file. Since the first line of each file contains the sequence length information, such as described:
@SRR3003130.1 HWI-ST741:596:H5FMVBCXX:1:1101:1244:1952 length=51
How do I pick the length=51, the 51 from this and feed in into the following command's --seqlength parameter:
./findtail --input_file Rrp6_S38_all_R1_001_egal.fastq --seqlength 51 \ --endgap 5 --taillength 10 --identity 100 --ptype A --stype T \ --output_format fasta --output_type pr > pr.fasta
The tool's command that I'm using only requires us to enter --seqlength once. So I do not think that determining the length of each and every read in the fastq file is of any use. Just simply the length from the first line of first read would suffice.
If something is lacking from my question, please let me know how can I improve.