Template:ListUserTasks

[[{{{1}}}]]

|- | Great work | 10 July 2011 | 11 July 2011

|

Ieaaa!

| | {{{8}}} | One example of Request | Discarded |- | Reverse-engineering of bacterial gene regulatory networks | |

|

| | {{{8}}} | Reverse-engineering of bacterial gene regulatory networks | Closed |- | MET0027 | 26 July 2011 | 26 July 2011

|

MET0027 project QC analysis for Illumina Infinium Methylation array 27k.

| | {{{8}}} | MET0027 | Closed |- | venn diagram | 5 September 2011 | 5 September 2011

|

Venn diagram for 3 list of genes

| | {{{8}}} | Lluis Morey's chipseq (jul-2011) | Closed |- | Chipseq 1 | 1 August 2011 | 8 September 2011

|

Custom chipseq analysis following a Cell stem cell paper (Karimi MM et al. 2011)

| | {{{8}}} | Cosma Chipseq | Closed |- | The whole analysis | 10 September 2011 | 29 September 2011

|

| | {{{8}}} | Mympn gene re-annotation | Closed |- | chipseq | 6 September 2011 | 7 September 2011

|

- Zrf1-FLAG_24 vs Ctrl-FLAG_24

- Zrf1-FLAG_0 vs Ctrl-FLAG_0 - gene annotation x2

- gene ontology x2

| | {{{8}}} | Aloia's chipseq (ZRF1) | Closed |- | QC of input file | 21 September 2011 | 21 September 2011

|

QC was performed by using fastQC tool.

| | {{{8}}} | Assembly of Fly genomes | Closed |- | fastq filtering | 22 September 2011 | 22 September 2011

|

creating perl script to filter fastq file according to phred qual

| | {{{8}}} | Assembly of Fly genomes | Closed |- | Chip-seq basic analysis | 12 October 2011 | 13 October 2011

|

4 samples + 1 control

| | {{{8}}} | DYP30 chipseq | Closed |- | Chipseq 1 | 1 September 2011 | 17 October 2011

|

Standard chipseq on 2 samples vs 2 KO

| | {{{8}}} | Lopez chipseq | Closed |- | Standard chipseq | 27 July 2011 | 10 August 2011

|

2 sample vs 1 control

| | {{{8}}} | Lange's chipseq (phf19) | Closed |- | Standard chipseq | 27 July 2011 | 5 August 2011

|

Standard chipseq of 2 samples vs 1 control (Ig)

| | {{{8}}} | Sarah Kinkley's chipseq (spok1) | Closed |- | Gene annotation of peaks | 10 August 2011 | 10 August 2011

|

| | {{{8}}} | Sarah Kinkley's chipseq (spok1) | Closed |- | fastq filtering 2 | 28 September 2011 | 10 October 2011

|

Creating scripts for fastq filtering and removing "single" mate pairs

| | {{{8}}} | Assembly of Fly genomes | Closed |- | QC on filtered reads | 1 October 2011 | 5 October 2011

|

QC was done with fastqc

| | {{{8}}} | Assembly of Fly genomes | Closed |- | chipseq custom overlap | 14 October 2011 |

|

Size distribution of peaks.

Overlap between peaks of CDPY and CK4. Overlap between peaks of CK4 and 23K4. Overlap between peaks of CK4 and MSKK4.

Gene list of every sample.

| | {{{8}}} | DYP30 chipseq | Closed |- | Another try | 12 July 2011 | 13 July 2011

|

Done a lot

| | {{{8}}} | One example of Request | Discarded |- | sitepro and custom sitepro | 30 July 2011 | 5 August 2011

|

We used sitepro on peaks and we developed another strategy to implement a similar analysis but normalizing the signal. We compared against random TSS and random portion of the genome.

| | {{{8}}} | Lange's chipseq (phf19) | Closed |- | chipseq 1 | 1 August 2011 | 8 August 2011

|

Chipseq using Cosma IgG as control. Sample analyzed were Cbx6, RING_1B_KO_Cbx7 and EED_KO_Cbx7. We provided a special annotation extending the peaks to 5 kb.

| | {{{8}}} | Lluis Morey's chipseq (jul-2011) | Closed |- | chipseq 2 | 1 August 2011 |

|

Chipseq on EB9_RING1B, EB9_cbx4, EB9_cbx2 using EB9_IgG (EB9 cell lines). Genome of reference is mouse. We received sequences once per week...

| | {{{8}}} | Lluis Morey's chipseq (jul-2011) | Closed |- | gene-set enrichment | 21 October 2011 |

|

We used david website to check for enrichment in some gene sub-groups.

| | {{{8}}} | DYP30 chipseq | Closed |- | retrieve genes on TSS | 31 October 2011 | 3 November 2011

|

Researchers asked to retrieve genes with TSS overlapping the peaks and to overlap them.

| | {{{8}}} | DYP30 chipseq | Closed |- | The Bm1 role in muscle satellite cells | |

|

| | {{{8}}} | The Bm1 role in muscle satellite cells | Closed |- | Chipseq standard | 21 November 2011 | 23 November 2011

|

Standard chipseq of 2 saples vs IgG

| | {{{8}}} | LOX chipseq | Closed

... further results

"{{{1}}}" cannot be used as a page name in this wiki.