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Assign reads and otus to samples:
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From my understanding, Line 9 from above simply splits the raw data into equal sized files, but the total number of reads should remain constant.
cd /gscratch/grandol1/loc_ad2LRII_LocAd2_3_16_22/rawdata
wc -l LowReadLRII*
Should return 8x the number of paired end reads (2x for R1 and 4x for the structure of fastq files).
This returns: 21045424 33809712 total
Divided by 8: 26306784226214
Line 11 then reads through all of the split files and assigns each read to a sample (parsed), to PhiX or non target (phixOther), or a mid error (truemiderrors). The reads assigned to these should add up to the numbers above.
wc -l parsed*
Returns: 1537123225644064 total
Divided by 8: 1921404 3205508 assigned to samples.
Assigned/Total (*100) = percent assigned: ~73%~76%
The target for samples was 83% (Off target by 12%)80%.
Things get more confusing with the phixOther and truemiderror files, because they do not appear to be true fastq files nor do they appear to be Fasta. So, I do not know how to count reads.
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For locad2:
wc -l locad2*
Returns: 407128018304944 total
The file formats appear the same as the “parsed*” files above.
Divided by 8: 5089102288118
For LRII:
wc -l LRII*
Returns: 112999527339120 total
Divided by 8: 1412494917390
LRII + locad2: 1921404
Even if all the unassigned reads are from locad2, this does not fix the expected ration of 2lo:1LR.
[508910+(2630678-1921404)] = 1218184 total possible locad2 reads
2288118+917390= 3205508
Same as the parsed read count above.
cd /project/microbiome/data_queue/seq/loc_ad2/tfmergedreads
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