Alignment Results

[arcolombo698]

Hello.

Are these results good for a library type fr-firststrand ?
I have a stranded library type and can't use library type UNSTRANDED.
so if the first strand is not good, then I need to use the second strand.
Thank you

Left reads:
Input : 30681699
Mapped : 13979559 (45.6% of input)
of these: 514390 ( 3.7%) have multiple alignments (4103 have >20)
Right reads:
Input : 30681699
Mapped : 13850738 (45.1% of input)
of these: 437904 ( 3.2%) have multiple alignments (4119 have >20)
45.4% overall read mapping rate.

Aligned pairs: 12729336
of these: 392039 ( 3.1%) have multiple alignments
77344 ( 0.6%) are discordant alignments
41.2% concordant pair alignment rate.

[GenoMax]

What kind of QC have you done? Were these reads trimmed/cleaned before the alignments?

[arcolombo698]

yes all were passed in QC. this is RNAseq, so you ignore the high duplications.
I ran it as single stranded library type firststrand, and am running the secondstrand library type now for comparison.