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Can I use the SRA spot lenght (AvgSpotLen) as the read lenght?

Hello,

I was looking a this post: What Is A "Spot" In Sra Format regarding what is as SPOT in the SRA format and a doubt arised for me, althought I still a lit bit confused of what is the SPOT

Can I use the AvgSpotLen, provided by SRA as the read lenght for my dataset? I say that because apparently "The spot length is the expected total length for all reads (used as a check to make sure we have all the data)."

Thanks.

illumina geo sra
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updated by GenoMax GenoMax • written by vitor • vitor

Probably. If it matches a query that you can do using Entrezdirect like so:

$ esearch -db sra -query SRR8523633 | efetch -format runinfo | awk -F "," '{OFS="\t"}{print $1,$4,$7}'
Run     spots   avgLength
SRR8523633      1191866 7229

This is a oxford nanopore dataset so the avg read length is long.

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written by GenoMax GenoMax

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