Hi, if my input seq are paired end reads, should I also add "--paired "?
My code is :
_python run-bwa.py A033.R1_kneaddata_paired_1.fastq A033.R1_kneaddata_paired2.fastq --fungi --output output/A033fungi.sam
No matter I add or don't add "--paired ", the .sam file will be very small, and after I run 'python compute-abundances.py', i will get one txt file with only one line "@@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE"
Below is the running info in the screen.
_[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 69706 sequences (10000282 bp)...
[M::process] read 69560 sequences (10000089 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 158, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (25, 122, 242)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 676)
[M::mem_pestat] mean and std.dev: (154.61, 129.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 893)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[mem_sampe] paired reads have different names: "A01066:85:H5G3LDMXY:1:1101:2899:1000:N:0:TAGTGGAAGC+NATAGGTACT#0", "A01066:85:H5G3LDMXY:1:1101:13575:1016:N:0:TAGTGGAAGC+TATAGGTACT#0"
I also want to ask how to merge the abundance txt files of many samples after I run 'python compute-abundances.py' for each sample?
Hi, if my input seq are paired end reads, should I also add "--paired "? My code is : _python run-bwa.py A033.R1_kneaddata_paired_1.fastq A033.R1_kneaddata_paired2.fastq --fungi --output output/A033fungi.sam
No matter I add or don't add "--paired ", the .sam file will be very small, and after I run 'python compute-abundances.py', i will get one txt file with only one line "@@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE"
Below is the running info in the screen. _[M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 69706 sequences (10000282 bp)... [M::process] read 69560 sequences (10000089 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 158, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (25, 122, 242) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 676) [M::mem_pestat] mean and std.dev: (154.61, 129.99) [M::mem_pestat] low and high boundaries for proper pairs: (1, 893) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [mem_sampe] paired reads have different names: "A01066:85:H5G3LDMXY:1:1101:2899:1000:N:0:TAGTGGAAGC+NATAGGTACT#0", "A01066:85:H5G3LDMXY:1:1101:13575:1016:N:0:TAGTGGAAGC+TATAGGTACT#0"
I also want to ask how to merge the abundance txt files of many samples after I run 'python compute-abundances.py' for each sample?
Thanks!