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Old 10-20-2016, 07:33 AM   #1
SDPA_Pet
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Default The number of raw reads

Hello, I am gonna make a table to do some stats of my Illumina pair-end sequencing.

There is a column (The number of raw reads). This is pair-end sequencing. If I got 10 million from R1 and I will have 10 million from R2. When I say the number of raw reads. should I put 10 million or 20 million (R1+R2).

Thanks
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Old 10-20-2016, 10:07 AM   #2
husamia
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for pre-alignment counts you could count the number of lines in the FASTQ files and divide by 4. I use wc -l
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Old 10-20-2016, 10:08 AM   #3
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Originally Posted by SDPA_Pet View Post
Hello, I am gonna make a table to do some stats of my Illumina pair-end sequencing.

There is a column (The number of raw reads). This is pair-end sequencing. If I got 10 million from R1 and I will have 10 million from R2. When I say the number of raw reads. should I put 10 million or 20 million (R1+R2).

Thanks
Illumina "ac"counts for them as 20M reads in their spec sheets (but they come from 10M unique clusters).
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Old 10-20-2016, 10:10 AM   #4
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for pre-alignment counts you could count the number of lines in the FASTQ files and divide by 4. I use wc -l
I have software to count. That's not a problem. Here is what I am concern. Should I add them number together after I get the number of R1 and R2 reads.
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Old 10-20-2016, 10:19 AM   #5
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Originally Posted by SDPA_Pet View Post
I have software to count. That's not a problem. Here is what I am concern. Should I add them number together after I get the number of R1 and R2 reads.
if R1 and R2 are the paired sequences, then should be count R1 = count R2 = number of clusters
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Old 10-20-2016, 10:22 AM   #6
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Originally Posted by husamia View Post
if R1 and R2 are the paired sequences, then should be count R1 = count R2 = number of clusters
I know. I mean when I report the total number of raw reads? should I report the number of clusters or the number of R1 or R2 X2.

I know the theory behind this. I am asking here is about which way the normal way to report the raw reads.
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Old 10-20-2016, 10:38 AM   #7
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Originally Posted by SDPA_Pet View Post
I know. I mean when I report the total number of raw reads? should I report the number of clusters or the number of R1 or R2 X2.

I know the theory behind this. I am asking here is about which way the normal way to report the raw reads.
If you want to track how many fragments were sequenced then at the cluster level. If you want to count total number of reads that came from a lane then at R1+R2 level.
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Old 10-20-2016, 11:29 AM   #8
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If you want to track how many fragments were sequenced then at the cluster level. If you want to count total number of reads that came from a lane then at R1+R2 level.
HI GenoMax,

Thanks. Besides BBTools, do you know any other software can check some basic information about assembled genomes/metagenomes data files. For example, some basic information such as total number contigs, N50, largest contigs, etc.
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Old 10-20-2016, 11:44 AM   #9
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HI GenoMax,

Thanks. Besides BBTools, do you know any other software can check some basic information about assembled genomes/metagenomes data files. For example, some basic information such as total number contigs, N50, largest contigs, etc.
Try QUAST/MetaQUAST.

Last edited by GenoMax; 10-20-2016 at 11:50 AM.
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Old 10-20-2016, 02:49 PM   #10
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Anyother software. I don't like this much
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