number reads fastq

Question

[fabbri.marco]

I am analysing a cancer panel. I am looking atf a number of reads for each fastq in the same flowcells. I have seen a difference in the number od reads when I have to start to worry? below tthe table:

file    num reads   percentage
1_S1_L001_R1_001.fastq.gz   1001223 2.58924706156174
1_S1_L001_R2_001.fastq.gz   1001223 2.58924706156174
10_S8_L001_R1_001.fastq.gz  1456083 3.76555335738392
10_S8_L001_R2_001.fastq.gz  1456083 3.76555335738392
11_S9_L001_R1_001.fastq.gz  1074256 2.77811655481852
11_S9_L001_R2_001.fastq.gz  1074256 2.77811655481852
12_S10_L001_R1_001.fastq.gz 1697460 4.38977462275496
12_S10_L001_R2_001.fastq.gz 1697460 4.38977462275496
13_S11_L001_R1_001.fastq.gz 2144491 5.54583446474521
13_S11_L001_R2_001.fastq.gz 2144491 5.54583446474521
14_S12_L001_R1_001.fastq.gz 2536390 6.55931830818366
14_S12_L001_R2_001.fastq.gz 2536390 6.55931830818366
2_S2_L001_R1_001.fastq.gz   1686737 4.3620440410153
2_S2_L001_R2_001.fastq.gz   1686737 4.3620440410153
3_S3_L001_R1_001.fastq.gz   1112423 2.87681963355186
3_S3_L001_R2_001.fastq.gz   1112423 2.87681963355186
4_S4_L001_R1_001.fastq.gz   1453481 3.75882436608609
4_S4_L001_R2_001.fastq.gz   1453481 3.75882436608609
6_S5_L001_R1_001.fastq.gz   1645281 4.25483533108344
6_S5_L001_R2_001.fastq.gz   1645281 4.25483533108344
7_S6_L001_R1_001.fastq.gz   1161745 3.00437048243402
7_S6_L001_R2_001.fastq.gz   1161745 3.00437048243402
9_S7_L001_R1_001.fastq.gz   1313106 3.39580278521277
9_S7_L001_R2_001.fastq.gz   1313106 3.39580278521277
Undetermined_S0_L001_R1_001.fastq.gz    1051574 2.71945899116852
Undetermined_S0_L001_R2_001.fastq.gz    1051574 2.71945899116852

[WouterDeCoster]

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Answer 1

[WouterDeCoster]

The abundance of the reads is more or less the consequence of the pooling used in the library prep. If you add twice as much of sample A you'll get twice as much reads. Ideally, you would determine the concentration of each library prior to pooling and perform the pooling equimolarly.

This probably isn't anything to worry about. You didn't tell us anything about your application, but the difference between the samples isn't too bad. If you are going to do variant calling this should be fine.