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Old 05-15-2018, 11:53 AM   #1
Name_less_
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Default Chip-seq data questions

Hello
I need work with Chip-seq of 3 conditions (WT, C and V). It’s single-end.
When I saw the data, questions born:

1. Each sample has duplicate, but each duplicate has 4 fastq files corresponding to “lanes” of the sequencing. That’s mean that the 4 files correspond to one sample? If so... Would I join the 4 fastq files for work with them as one sample?

2. Other sequencing data are present, with names WTIN, CIN and VIN (each one with 4 fastq files). The text file that I received says: “Each experiment was performed in duplicate, the sequencing was through NextSeq with a 76ntSR reading format, single entry income for each sample marked as WTIN, CIN and VIN.” Someone known whats that mean?

Thanks to everyone!
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Old 05-16-2018, 02:33 AM   #2
nucacidhunter
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1- Libraries has been sequenced on a NextSeq flow cell that has 4 lanes so the data from lanes for each library needs to be merged into one file for each sample replicates for analysis.

2- You need to clarify this with data supplier. The terms "WTIN, CIN and VIN" simply could refer to your sample names for WT, C and V, respectively. I would normally name them as WTIN_1, WTIN_2 ... to identify each replicate.
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Old 05-22-2018, 06:37 AM   #3
Name_less_
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Quote:
Originally Posted by nucacidhunter View Post
1- Libraries has been sequenced on a NextSeq flow cell that has 4 lanes so the data from lanes for each library needs to be merged into one file for each sample replicates for analysis.

2- You need to clarify this with data supplier. The terms "WTIN, CIN and VIN" simply could refer to your sample names for WT, C and V, respectively. I would normally name them as WTIN_1, WTIN_2 ... to identify each replicate.
Thank you! So I will merge the fastq files.
Referent to point 2:
I have 9 folders, 2 for each replicate (WT1, WT2, C1, C2, V1, V2) and other three (WTIN, CIN, VIN). I talked with my friend and he told me that, possibly, the WTIN, CIN and VIN correspond to control of sequencing. So, I will take some reads sequence and will make Blast.
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