In principle I see no issues with mixing dual and single index TruSeq libraries in the same run. The result will be that for the i7 read, the normal single-index sequence will be collected along with an extra 2 bases. For indexes 1-12, these last 2 bases will always be "AT".
I think their i7 sequences (as would be entered in the sample sheet would be as follows) :
>TruSeq_Single_Index_1
ATCACGAT
>TruSeq_Single_Index_2
CGATGTAT
>TruSeq_Single_Index_3
TTAGGCAT
>TruSeq_Single_Index_4
TGACCAAT
>TruSeq_Single_Index_5
ACAGTGAT
>TruSeq_Single_Index_6
GCCAATAT
>TruSeq_Single_Index_7
CAGATCAT
>TruSeq_Single_Index_8
ACTTGAAT
>TruSeq_Single_Index_9
GATCAGAT
>TruSeq_Single_Index_10
TAGCTTAT
>TruSeq_Single_Index_11
GGCTACAT
>TruSeq_Single_Index_12
CTTGTAAT
>TruSeq_Single_Index_13
AGTCAACA
>TruSeq_Single_Index_14
AGTTCCGT
>TruSeq_Single_Index_15
ATGTCAGA
>TruSeq_Single_Index_16
CCGTCCCG
>TruSeq_Single_Index_18
GTCCGCAC
>TruSeq_Single_Index_19
GTGAAACG
>TruSeq_Single_Index_20
GTGGCCTT
>TruSeq_Single_Index_21
GTTTCGGA
>TruSeq_Single_Index_22
CGTACGTA
>TruSeq_Single_Index_23
GAGTGGAT
>TruSeq_Single_Index_25
ACTGATAT
>TruSeq_Single_Index_27
ATTCCTTT
Then the i5 read will always be "TCTTTCCC" -- as that is the segment of the left adapter that would be addressed by the dual index primer for i5.
I brought this up in a previous thread. Therein, a poster, "Vinz", specified exactly what to do in a manner so succinct I had no idea how to interpret it.
Note: this post contains information partially derived from the Illumina Customer Sequence Letter. Illumina specifies in that letter that they give limited permission to "distribute the sequence information outside your institution or to publish the sequence information in presentations, manuscripts, or publications authored by you, as long as it is accompanied by the following copyright notice:"
Oligonucleotide sequences © 2007-2012 Illumina, Inc. All rights reserved.
--
Phillip
I think their i7 sequences (as would be entered in the sample sheet would be as follows) :
>TruSeq_Single_Index_1
ATCACGAT
>TruSeq_Single_Index_2
CGATGTAT
>TruSeq_Single_Index_3
TTAGGCAT
>TruSeq_Single_Index_4
TGACCAAT
>TruSeq_Single_Index_5
ACAGTGAT
>TruSeq_Single_Index_6
GCCAATAT
>TruSeq_Single_Index_7
CAGATCAT
>TruSeq_Single_Index_8
ACTTGAAT
>TruSeq_Single_Index_9
GATCAGAT
>TruSeq_Single_Index_10
TAGCTTAT
>TruSeq_Single_Index_11
GGCTACAT
>TruSeq_Single_Index_12
CTTGTAAT
>TruSeq_Single_Index_13
AGTCAACA
>TruSeq_Single_Index_14
AGTTCCGT
>TruSeq_Single_Index_15
ATGTCAGA
>TruSeq_Single_Index_16
CCGTCCCG
>TruSeq_Single_Index_18
GTCCGCAC
>TruSeq_Single_Index_19
GTGAAACG
>TruSeq_Single_Index_20
GTGGCCTT
>TruSeq_Single_Index_21
GTTTCGGA
>TruSeq_Single_Index_22
CGTACGTA
>TruSeq_Single_Index_23
GAGTGGAT
>TruSeq_Single_Index_25
ACTGATAT
>TruSeq_Single_Index_27
ATTCCTTT
Then the i5 read will always be "TCTTTCCC" -- as that is the segment of the left adapter that would be addressed by the dual index primer for i5.
I brought this up in a previous thread. Therein, a poster, "Vinz", specified exactly what to do in a manner so succinct I had no idea how to interpret it.
Note: this post contains information partially derived from the Illumina Customer Sequence Letter. Illumina specifies in that letter that they give limited permission to "distribute the sequence information outside your institution or to publish the sequence information in presentations, manuscripts, or publications authored by you, as long as it is accompanied by the following copyright notice:"
Oligonucleotide sequences © 2007-2012 Illumina, Inc. All rights reserved.
--
Phillip
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