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Trying to estimate genome size - no peak in jellyfish kmer abundance plot
Hi all,
I have some 2 X 100 PE Illumina genomic data from a marine invertebrate whose genome size I'd like to estimate. I was trying to follow the workflow presented here.
I ran the following commands on the data:
I didn't save the output but the histogram I got didn't have a peak in it. kmers with an abundance of 1 were the most abundant, kmers with an abundance of 2 were the second most abundant and so on. I tried this with a kmer of 15 and got the same result. I thought my data might be too dirty so I tried to clean them up pretty strictly:
This left me with 36,530,479 reads that should be very high quality. Again, I didn't see a peak in the resulting histogram (just the first 2,000 lines):
I had a similar pattern when I tried a kmer of 15 in Jellyfish.
Here's the output of stats.txt from Jellyfish:
For the sake of genome size estimation, should I assume these are all "real" kmers? Does something seem wrong with the data? Do I just not have enough data? I'm basically just confused about how to move forward. I'm also trying to follow the equation presented in this thread:
N = M/((L-k+1)/L) but I don't know how to calculate M given this result.
Any advice would be greatly appreciated.
Kevin
I have some 2 X 100 PE Illumina genomic data from a marine invertebrate whose genome size I'd like to estimate. I was trying to follow the workflow presented here.
I ran the following commands on the data:
Code:
jellyfish count -m 31 -o output -c 3 -s 20M -t 32 test.fastq jellyfish merge -o output.jf output\_* jellyfish histo -f output.jf > histogram.txt jellyfish stats -v -o stats.txt output.jf
Code:
fastq_quality_filter -q 35 -p 95 -Q33 -i test.fastq | fastq_quality_trimmer -t 35 -l 15 -Q33 | fastx_trimmer -f 11 -m 15 -o test_1.fastq -Q33 fastqc test_1.fastq jellyfish count -m 31 -o output -c 3 -s 20M -t 32 test_1.fastq jellyfish merge -o output.jf output\_* jellyfish histo -f output.jf > histogram.txt jellyfish stats -v -o stats.txt output.jf
Code:
1 111406305 2 44787641 3 35663255 4 30110672 5 25687529 6 21730391 7 18148846 8 14888556 9 11975686 10 9424344 11 7288086 12 5561574 13 4194056 14 3145730 15 2366083 16 1787055 17 1363102 18 1057096 19 839650 20 680629 21 565372 22 475216 23 403603 24 349056 25 304122 26 268808 27 237640 28 211297 29 189093 30 171082 31 154639 32 139571 33 126843 34 116969 35 109347 36 100717 37 93669 38 87123 39 81720 40 76061 41 71863 42 67541 43 63722 44 60141 45 57254 46 54727 47 51908 48 49099 49 46783 50 44553 51 42134 52 40393 53 38655 54 37058 55 35593 56 34344 57 32965 58 31422 59 30706 60 29415 61 27846 62 27213 63 25761 64 24730 65 24015 66 23362 67 22404 68 21747 69 20826 70 20495 71 19574 72 19310 73 18386 74 18096 75 17403 76 17154 77 16396 78 15919 79 15682 80 15002 81 14852 82 14402 83 13726 84 13532 85 13040 86 12793 87 12622 88 12165 89 11894 90 11585 91 11246 92 10888 93 10685 94 10534 95 10185 96 10118 97 10086 98 9830 99 9671 100 9201 101 9175 102 9137 103 8790 104 8739 105 8476 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Here's the output of stats.txt from Jellyfish:
Code:
k-mer length (bases): 31 value length (bytes): 4 max reprobe : 1953 hash size : 33554432 Unique: 111406305 Distinct: 358698199 Total: 2179950654 Max_count: 398226
N = M/((L-k+1)/L) but I don't know how to calculate M given this result.
Any advice would be greatly appreciated.
Kevin
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