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I am new in our lab and I am going to do bulk RNA-Seq. What type of files will we get from the company (Genewiz)? Will it be a bunch of Fastq files? or they give something like bam files?
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1$\begingroup$ Welcome to the site. Genewiz is a commercial company which you are outsourcing to and I strongly recommend contacting them directly. Essentially you are paying for this service so I think it is fair to request this information directly. Their contact details are here azenta.com/contact-us ... The implications of the question is that this site provides technical support for a commercial entity. $\endgroup$– M__ ♦Aug 3 at 22:59
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$\begingroup$ Please do not cross-post biostars.org/p/9571387 and if you do at least leave a comment with the cross-reference. It's just double effort for people in both communities, especially for these sorts of very basic questions. $\endgroup$– ATpointAug 4 at 7:48
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$\begingroup$ OP has deleted their post on biostars. $\endgroup$– Ram RSAug 6 at 18:09
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1 Answer
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This cannot be predicted unless you have interacted with them previously. Most commonly a sequencing facility will send raw data as gzipped fastq files, often together with md5 checksums so the user can check file integrity after transfer/download from them.
We worked with a facility before who sent data in unaligned bam format, which then for typical workflows first had to be converted back to fastq.
After all, you're a paying customer so feel free to shoot them an email and ask whatever question comes up. Ask what exactly they will provide so that you can prepare your workflows accordingly. Most likely it will be fastq.gz.
