In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library?

Not the median fragment length but the maximum fragment length you expect. However, you will see that in illumina sequencers, the longer the fragments are the less efficiently they are sequenced so long fragment length pairs are not very numerous.

Persistent URL

Resource purlPURL: https://gxy.io/GTN:F00255

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