What to do with corrupted lane files

Question

[pentium3-user]

Hi,
I have paired-end RNASeq data from 2 conditions with each 3 replicates from 2 lanes (lane04 and lane05). So I have 24 files.

Unfortunately 3 files of lane04 are corrupted and cannot be restored. So what do you think is the best strategy?

• Using only lane05
• Merging the healthy samples and normalize the read counts?
• using just the replicates with healthy files in both lanes?
• something else?

The corrupted files are

• lane04 Condtion 1 replicate 1 2nd pair
• lane04 Condtion 1 replicate 2 1st pair
• lane04 Condtion 1 replicate 2 2nd pair

Any other files are healthy.

Please note that I'm currently using only lane05 but this gives some strange results (see this post). Of course I don't know if this is related to the decision of using only lane05 but I try to eliminate all steps with are possible related to this issue.

I'm very thankful for any help I get.

[GenoMax]

Unfortunately 3 files of lane04 are corrupted and cannot be restored.

Did the corruption happened locally on your end? Generally sequence providers should keep a backup copy of your data for some time (we do for 3 yrs). You may need to pay for them to restore a copy but have you tried to ask?