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Old 07-12-2019, 01:06 PM   #5
SDPA_Pet
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Location: US

Join Date: Apr 2013
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Quote:
Originally Posted by GenoMax View Post
What does that mean? Is the data pretrimmed, which is why you have much shorter reads than expected? If all reads are 150 bp, sequencing facility may have made an error with run setup, if you had requested 2 x 300 bp.
"What does that mean?" -- This is new sequencing center that I recently changed. It's first time that I used. "sloppy work" means they didn't do a good job and something wrong about the sequencing chemistry and sequencing process.

"Is the data pretrimmed". I doubt it is pre-trimmed. They only gave me 2 files. One forward fastq file and one reverse fastq file. If they have do some trimming or analysis, sequencing center would give you 4 files another two files would be F and R fastq files after trimming.

"If all reads are 150 bp, sequencing facility may have made an error with run setup" -- Yes, all reads are 150bp. When you said made an error, do you mean their setting wrong? for example, 2X300bp should run 300 runs. they only run 150 cycles? The machine suddenly stopped or wrong settings. Or do you mean they use wrong prep kits? for example, Hiseq commonly does 2X150bp or 2X250 bp? They use hiseq prep kits?

Last edited by SDPA_Pet; 07-12-2019 at 01:14 PM.
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