Hi, thanks for your efforts to share such convenient pipeline.
- Recently, I am learning the strainphlan. I have one question as below:
How to creat sam.bz2 with already run metaphlan3 with the output of profile.txt and bowtie2 file?
ps, i have run the run metaphlan3 with the output of profile.txt and bowtie2 file, but not sam file before for a large batch of samples. When I want to run strainphlan, do I have to rerun the metphlan again at the first step, or is there any possibility that I can create sam.bz2 based on already run metaphlan with the output of profile.txt and bowtie2 file?
- I have try to use the bowtie2 as input file and rerun the metaphlan3, as below:
“metaphlan ./007-MT3_S102_L002.bowtie2.bz2 --input_type bowtie2out --read_min_len 70 --bowtie2db ./Ref_db/MetaPhlAn --index mpa_v30_CHOCOPhlAn_201901 --bt2_ps very-sensitive --min_cu_len 2000 --tax_lev a --avoid_disqm --stat_q 0.2 --stat tavg_g -t rel_ab_w_read_stats --unknown_estimation --add_viruses -o ./007-MT3_S102_L002.txt -s ./007-MT3_S102_L002.sam.bz2 --sample_id 007-MT3_S102_L002 --nproc 32”
Also, I have try to use bowtie2 with fastq as input file to ouput sam, as below:
“bowtie2 -p 6 -3 5 --local -x ./Ref_db/MetaPhlAn/mpa_v30_CHOCOPhlAn_201901 -1 ./MT3/007-MT3_S102_L002_R1_001_kneaddata_paired_1.fastq -2 ./MT3/007-MT3_S102_L002_R1_001_kneaddata_paired_2.fastq -S 007-MT3.sam.bz2”
But I found that both the output sam file is bigger than the file produced by the metaphlan (input: fastq, output with profile, sam, and bowtie2).
Any suggestion or comments. Many thanks!