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Forum: Bioinformatics 12-19-2019, 10:48 PM
Replies: 0
Views: 910
Posted By paolo.kunder
Ampli1™ LowPass kit for Illumina

Dear All,

I would like to set up a pipeline to analyze data obtained with the following kit

Ampli1™ LowPass kit for Illumina
...
Forum: Bioinformatics 02-07-2017, 09:56 AM
Replies: 11
Views: 1,557
Posted By paolo.kunder
Question Ops I was wrong, my data is full of yRNA, no idea...

Ops I was wrong, my data is full of yRNA, no idea why...and what they are..
Forum: Bioinformatics 02-06-2017, 09:06 AM
Replies: 11
Views: 1,557
Posted By paolo.kunder
Dont you think that this is the spike in from...

Dont you think that this is the spike in from Exiqon that was added in the samples?
Forum: Bioinformatics 02-06-2017, 07:48 AM
Replies: 11
Views: 1,557
Posted By paolo.kunder
No human unfortunately......

No human unfortunately......
Forum: Bioinformatics 02-06-2017, 07:43 AM
Replies: 11
Views: 1,557
Posted By paolo.kunder
I did it, i trimmed adaptor from my reads and...

I did it, i trimmed adaptor from my reads and blasted.
90% of my reads blast an intronic region conserved in multiple species..
Forum: Bioinformatics 02-06-2017, 07:38 AM
Replies: 11
Views: 1,557
Posted By paolo.kunder
Exactly. It match a pretty conserved intronic...

Exactly. It match a pretty conserved intronic region of 32 bp in multiple species..
I assume this is spike in..
Forum: Bioinformatics 02-06-2017, 02:26 AM
Replies: 11
Views: 1,557
Posted By paolo.kunder
small RNA Seq adapter trimming

Dear All,
I am new to small RNA Seq data.
I have just received data and before I map my samples I would like to remove 5 and 3' adapters.
Here is my FastQC output, is similar in all samples:
...
Forum: Academic/Non-Profit Jobs 08-02-2016, 12:50 AM
Replies: 0
Views: 885
Posted By paolo.kunder
Junior Bioinformatician position - Humanitas - Milan/Italy

“Junior Bioinformatician position in the Immunology Research Area at Humanitas Research Hospital”

We are seeking a highly motivated young graduate student with strong interest in high throughput...
Forum: Sample Prep / Library Generation 11-23-2015, 05:51 AM
Replies: 10
Views: 1,199
Posted By paolo.kunder
these may help you?

these may help you?
Forum: Sample Prep / Library Generation 11-23-2015, 05:39 AM
Replies: 10
Views: 1,199
Posted By paolo.kunder
so is definitely a bad library preparation? I...

so is definitely a bad library preparation?
I have to be sure before going to complain to the service!
Forum: Sample Prep / Library Generation 11-23-2015, 05:34 AM
Replies: 10
Views: 1,199
Posted By paolo.kunder
and moreover, why should I have more than 300'000...

and moreover, why should I have more than 300'000 reads 32bp long,

I have demultiplexed the data, with the following adapters

index
TCCGGAGA
CGCTCATT
ATTACTCG
GAGATTCC
ATTACTCG
Forum: Sample Prep / Library Generation 11-23-2015, 05:28 AM
Replies: 10
Views: 1,199
Posted By paolo.kunder
Yes this is Illumina NextSeq500 data, I am a...

Yes this is Illumina NextSeq500 data,
I am a bit confused, why they should be of different length after trimming?
I analyzed many RNA Seq data of Hiseq and they are all (100%) the same length, I...
Forum: Sample Prep / Library Generation 11-23-2015, 05:12 AM
Replies: 10
Views: 1,199
Posted By paolo.kunder
reads of different size - RNA SEQ

Dear All,
I have just received some RNA Seq data and I noticed that not all reads are at the size I expected: (75bp)
only 64 % are at the correct size,
what should I do? Should I remove all reads...
Forum: Bioinformatics 09-04-2015, 02:28 AM
Replies: 4
Views: 1,632
Posted By paolo.kunder
Genome option should be genome build, for example...

Genome option should be genome build, for example hg19...mm10..
Forum: Academic/Non-Profit Jobs 07-22-2015, 11:52 PM
Replies: 0
Views: 625
Posted By paolo.kunder
Junior Bioinformatic position - Humanitas - Italy

Junior Bioinformatic position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas
Contact person: Dr. Paolo Kunderfranco
Contact email:...
Forum: Academic/Non-Profit Jobs 07-03-2015, 06:05 AM
Replies: 0
Views: 745
Posted By paolo.kunder
PhD position in Bioinformatic at Humanitas Reseacrh Center - Milano - Italy

Bioinformatic position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas:

We are seeking a highly motivated young PhD student with strong interest in high...
Forum: Bioinformatics 10-03-2014, 12:10 AM
Replies: 2
Views: 1,825
Posted By paolo.kunder
Is normal, you are using scale="row", so the...

Is normal, you are using scale="row", so the values in each row are centered and scaled. With two samples, you wil get only two colours.

Try with scale="none", or to add more samples in your...
Forum: Academic/Non-Profit Jobs 09-15-2014, 12:15 AM
Replies: 0
Views: 1,176
Posted By paolo.kunder
Bioinformatics position-Humanitas-Milano-Italy

Bioinformatics position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas:
...
Forum: Bioinformatics 07-31-2014, 03:21 AM
Replies: 0
Views: 826
Posted By paolo.kunder
bowtie2 -M option

Dear All,

I am using bowtie version 2.2.2 and I would like to set an option that is still in use in bowtie.



I tried to run bowtie2 with -M option and this warning appears:
Forum: Bioinformatics 07-25-2014, 01:39 AM
Replies: 2
Views: 1,152
Posted By paolo.kunder
In MACS README file is well explained: ...

In MACS README file is well explained:

http://liulab.dfci.harvard.edu/MACS/00README.html

NAME_peaks.xls is a tabular file which contains information about called peaks.

NAME_peaks.bed is...
Forum: Bioinformatics 02-21-2014, 12:22 AM
Replies: 7
Views: 2,152
Posted By paolo.kunder
LINE(long interspersed nuclear element) RNA Seq

Dear All,

I would like to analyze in a dataset of RNA Seq the expression of LINE1 transcripts ( called L1 ORF).
I would like to share with you any idea in the piepeline I may use.

I tried to...
Forum: Sample Prep / Library Generation 12-12-2013, 10:39 PM
Replies: 5
Views: 7,392
Posted By paolo.kunder
Adaptor dimer contamination

Dear All,

We are facing some problems with adaptor dimers in Illumina RNA seq library prep.

There is a small amount of adaptor dimer (at ~150 bp) in a few of the samples. We tried a second...
Forum: Bioinformatics 10-17-2013, 07:26 AM
Replies: 6
Views: 2,938
Posted By paolo.kunder
I think you need to install it, anyway some...

I think you need to install it,
anyway some other suggestions?
Forum: Bioinformatics 10-15-2013, 10:53 PM
Replies: 6
Views: 2,938
Posted By paolo.kunder
Honestly I would like to avoid installing Galaxy...

Honestly I would like to avoid installing Galaxy in my server, any other suggestion?
Forum: Bioinformatics 10-15-2013, 05:29 AM
Replies: 6
Views: 2,938
Posted By paolo.kunder
tag density distribution over the gene body

Dear All,

I have a bam file of a MeDIP seq sample.
I have also a bed file of all mouse genes.

I would like to plot the tag density over the genebody as illustrated in this two examples I found...
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