Hi to everyone,
beforehand: I'm quite new to Linux and also the whole Assembly.
I received my Next-Gens Seq files from Eurofins. Method was Illumina Paired-End 2*150. The two files are each almost 10 million sequences long in fastq.
Somehow I managed to run SPAdes with my two files.
Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['xx1.fastq'] right reads: ['xx2.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: xx/tmp Threads: 16 Memory limit (in Gb): 15
(1) Are those parameters right? I don't get the difference between the paired-end mode, mate-paired and interlaced. We ordered Paired-End seq and I received 2 files called xx_1.fastaq.gz and xx_2.fastaq.gz Since I got two files I think thy are not interlaced, am I right. What's with the other modes and another point. are my fiels fr, rf or ff? I don't even know where to get this information from.
(2) If my parameters are right and SPAdes run through my files I want to map them with Bowtie2. i indexed my reference genome. But what files from SPAdes should I take for that? . I assume the contig.fasta, but what exactly is the scaffold.fasta and all the other files? So I ran bowtie2 with the following command and got this as output:
$ bowtie2 -x yy_REFERENCE -f -U xx/results/contigs.fasta -S yy/SAM/alignment_contigs.sam terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) (ERR): bowtie2-align exited with value 134
What does that mean? What is error value 134? I'm running Ubuntu 18.04 with 16 GB of RAM. I'm afraid that it means that I have to less RAM, is it possible? I also have access to several clusters with more CPU and RAM, but I have absolutely no clue how to run anything on them.
I had no problems running bowtie2 with the Lambda phage example files. It is also hard for me to find some information about all this. So I would really appreciate it, if someone of you have good books, papers or tutorials for that.
I know these are a lot of question, but I hope you can help me with that.
I'm looking forward to your answers. Kiluah