Vagelis Harokopos
3:07 PM (0 minutes ago)

to me 
Hi Martin,

For Ion 342 please proceed with the following groups/comparisons:

Mouse samples
Group 1 (4a)
YK3R1_5291 4a +
YK3R2_5291 4a +
YK3R3_5291 4a +

Group 2 (4a Ctrl)
YK3R4_5291 4a  -
YK3R5_5291 4a  -

Group 3 (4f)
YK3R6_5269 4f +
YK3R7_5269 4f +
YK3R8_5269 4f +

Group 4 (4f Ctrl)
YK3R9_5269 4f  -
YK3R10_5269 4f  -

Group 5
YK3R11_C+1+
Grp4aMinus_vs_Grp4aPlus
Grp4fMinus_vs_Grp4fPlus

Grp4aMinus4fMinus_vs_Grp4aPlus
Grp4aMinus4fMinus_vs_Grp4fPlus
Grp4aMinus4fMinus_vs_Cplus1Plus
-----------------------------------
Group 1 vs 2, 
Group 3 vs 4,
Group 1 vs 2+4,
Group 3 vs 2+4, 
Group 5 vs 2+4.
------------------------------------

Human samples
YK3R12_c+1 short huh7.5 
vs
YK3R13_vector huh7.5

If you need anything else contact me,
Vaggelis

#@
Dear Ioannis,

the check for the presence of the 4a and 4f sequences in the samples gave:

R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.IonXpress_001.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R10-5269-4fminus.IonXpress_034.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R11-Cplus-1plus.IonXpress_035.fastq
4a: 1  4f: 1
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R12-Cplus-shorthuh75.IonXpress_036.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R13-vectorhuh75.IonXpress_037.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R1-5291-4aplus.IonXpress_025.fastq
4a: 6  4f: 1
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R2-5291-4aplus.IonXpress_026.fastq
4a: 3  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R3-5291-4aplus.IonXpress_027.fastq
4a: 2  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R4-5291-4aminus.IonXpress_028.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R5-5291-4aminus.IonXpress_029.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R6-5269-4fplus.IonXpress_030.fastq
4a: 1  4f: 3
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R7-5269-4fplus.IonXpress_031.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R8-5269-4fplus.IonXpress_032.fastq
4a: 0  4f: 0
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R9-5269-4fminus.IonXpress_033.fastq
4a: 0  4f: 0

It seems 4a+,4a- and 4f- are ok.
For 4f+ I would use only the sample
R_2017_03_31_13_20_56_user_IONAS-342-DrKarakas_170330_YK3R1-13.YK3R6-5269-4fplus.IonXpress_030.fastq
and omit the other 2 as they do not contain 4f.

However the number of reads matching 4a or 4f is in general low and it could be these would be detected
with slightly deeper sequencing.

BW,
Martin