17 Feb
2012
17 Feb
'12
3:31 p.m.
Dear all,
here is our analysis of the miRNA samples of 4 institutes (UNIGE, MPIMG,
ICMB, CNAG, see attatched pdf file).
This is basically what I did:
1. trim reads to 36 bp (prinseq).
2. remove adapter sequence (cutadapt), split into trimmed reads and
untrimmed reads
3. remove polyA tails (cutadapt)
4. map trimmed reads against genome and miRNA reference (the one from
the FTP server).
5. count reads per miRNA
There are larger differences considering the amount of adapter sequences
within the samples and the library diversity.
best wishes,
Matthias
--
Matthias Barann
Institute of Clinical Molecular Biology
Christian Albrechts University Kiel
Schittenhelmstr. 12
D-24105 Kiel, Germany
m.barann(a)ikmb.uni-kiel.de
+49 - (0)431 - 597 8681 (office)
17 Feb
17 Feb
3:54 p.m.
Thanks a lot Matthias, this is great analysis.
In Geneva we will run another round of sequencing for our samples to
increase the coverage. I hope that Leiden, Uppsala and Munich have miRNA
data available really soon for QC, since the quality seems quite
variable and reruns may be necessary.
We just agreed to have an additional call on Tuesday (21st) at 3pm to
discuss the practicalities of miRNAseq quality with Philip, Matthias,
Marc and Esther. If someone else wants to attend, just let me know. Of
course we'll discuss the miRNAs also on the analysis group call next
Thursday.
best regards,
Tuuli
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen(a)unige.ch
On 2/17/12 3:31 PM, Matthias Barann wrote:
Dear all,
here is our analysis of the miRNA samples of 4 institutes (UNIGE,
MPIMG, ICMB, CNAG, see attatched pdf file).
This is basically what I did:
1. trim reads to 36 bp (prinseq).
2. remove adapter sequence (cutadapt), split into trimmed reads and
untrimmed reads
3. remove polyA tails (cutadapt)
4. map trimmed reads against genome and miRNA reference (the one from
the FTP server).
5. count reads per miRNA
There are larger differences considering the amount of adapter
sequences within the samples and the library diversity.
best wishes,
Matthias
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Geuvadis_rna_analysis(a)lists.crg.es
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4:06 p.m.
Hi,
I won't be available on the 21st at 15h, but Esther will conduct the
preliminary QC for Barcelona, so she can explain me later.
Best wishes,
Sergi
---------------------------------
Sergi Beltran Agulló
Bioinformatics Analysis Group
CNAG - National Center for Genomic Analysis
Parc Científic Barcelona - Torre I
Baldiri i Reixac 4, 2a p.
08028 Barcelona
(+34)934033748
sbeltrana(a)pcb.ub.cat
www.cnag.cat
---------------------------------
On 02/17/2012 03:54 PM, Tuuli Lappalainen wrote:
Thanks a lot Matthias, this is great analysis.
In Geneva we will run another round of sequencing for our samples to
increase the coverage. I hope that Leiden, Uppsala and Munich have
miRNA data available really soon for QC, since the quality seems quite
variable and reruns may be necessary.
We just agreed to have an additional call on Tuesday (21st) at 3pm to
discuss the practicalities of miRNAseq quality with Philip, Matthias,
Marc and Esther. If someone else wants to attend, just let me know. Of
course we'll discuss the miRNAs also on the analysis group call next
Thursday.
best regards,
Tuuli
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen(a)unige.ch
On 2/17/12 3:31 PM, Matthias Barann wrote:
Dear all,
here is our analysis of the miRNA samples of 4 institutes (UNIGE,
MPIMG, ICMB, CNAG, see attatched pdf file).
This is basically what I did:
1. trim reads to 36 bp (prinseq).
2. remove adapter sequence (cutadapt), split into trimmed reads and
untrimmed reads
3. remove polyA tails (cutadapt)
4. map trimmed reads against genome and miRNA reference (the one from
the FTP server).
5. count reads per miRNA
There are larger differences considering the amount of adapter
sequences within the samples and the library diversity.
best wishes,
Matthias
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
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2 comments
3 participants
participants (3)
-
Matthias Barann -
Sergi Beltran Agulló -
Tuuli Lappalainen