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aligning the develop with master
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fix for #583
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k3yavi committed Nov 12, 2020
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Expand Up @@ -42,7 +42,7 @@ below, assume we have two replicates ``lib_A`` and ``lib_B``. The left and righ
``lib_B`` are ``lib_B_cb.fq`` and ``lib_B_read.fq``, respectively. The following are both valid
ways to input these reads to alevin::

> salmon alevin -lISR -1 lib_A_cb.fq lib_B_cb.fq -2 lib_A_read.fq lib_B_read.fq
> salmon alevin -l ISR -1 lib_A_cb.fq lib_B_cb.fq -2 lib_A_read.fq lib_B_read.fq

Similarly, both of these approaches can be adopted if the files are gzipped as well::

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