Closed cabraham03 closed 8 months ago
If you pass in the reads SCAPP will do the alignment for you. Is that what you are asking about?
I'm just confused. First, i just want to know how to generate the appropriated fastg file, could I use a fastg generated with megahit or any other program ??? and then run SCAPP something like:
scapp -g k119.contigs.fastg -o Results_SCAPP -r1 file_R1.fastq -r2 file_R1.fastq
is that ok ? or how generate the fastg appropriated file ??? Thanks
That command looks fine in general, I would note the following issues:
When you generate the fastg you need to use the correct value of k. Assuming k is 119 since you are using k119.contigs.fa, the contigs2fastg command should be: megahit_toolkit contig2fastg 119 intermediate_contigs/k119.contigs.fa > k119.contigs.fastg
i.e. you need to use 119 as the value of k not 99.
SCAPP needs to know the value of the maximum k, so the command would be:
scapp -g k119.contigs.fastg -o Results_SCAPP -r1 file_R1.fastq -r2 file_R2.fastq -k 119
(also note that in the command you gave above you used file_R1.fastq twice instead of -r2 file_R2.fastq
).
thanks so much, it was an error in R1 and R2 sorry !! I will try how you describe for k 119 !!! just one more question, if a generate the BAM file, using bwa and samtools, could be used instead of r1 and r2, that's right ??? thanks for all !!!!
That is good, you will have to regenerate the fastg using 119 and add -k 119 as an option to SCAPP. If you already have a BAM file mapping the reads to the contigs you can use that using -b
Hi, sorry for the question, I'm trying to make my first analyses with metagenomics shotgun, and I want to try SCAPP to detect plasmids. I just made an assembly with megahit and then generate the fastg file, I just was wonder, in this case how can I generate the bam file using metagenomics, or if you have any pipeline that you can share to follow it:
This is mine; firts I made the trim in fastq files and then generate the assembly:
megahit -1 File_R1_trim.fastq -2 File_R2_trim.fastq --min-contig-len 1000 -m 0.8 -t 2 -o megahit
To create the fastg file, I use the last intermediate contigs (k119)
megahit_toolkit contig2fastg 99 intermediate_contigs/k119.contigs.fa > k119.contigs.fastg
my problem is, I want to generate the bam file, and I was looking for pipeline to generate the index for bwa, with genomics is easy for me, I just take a reference genome, but in this case with shotgun I'm lost !!!
and when I generate the index this is mi possible pipeline, just let me know if I'm ok with the next code:
bwa mem -t 80 bwa_index File_R1_trim.fastq File_R2_trim.fastq | samtools view -bS - > bwa.bam
any advice thanks