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Forum: Bioinformatics 03-06-2017, 02:04 AM
Replies: 1
Views: 1,368
Posted By edeka
smallRNA: how analyze

Hello!
I am new to smallRNA seq and I am a bit confused as to analyze my data (from human genome).
it is better to:
1) align against ncRNA transcriptome from Ensembl
2) align against genome
3)...
Forum: Bioinformatics 10-05-2016, 03:51 AM
Replies: 0
Views: 1,233
Posted By edeka
sorting reads

Hello!
I am trying to understand what are the differences between samtools sort, picard reordersam and sortsam.

Thank you in advance

best
Forum: Bioinformatics 10-04-2016, 02:38 AM
Replies: 0
Views: 2,461
Posted By edeka
vcf file hg 38

Hi! where I can fine the indels.vcf file (Mills and 1000G gold standard) for hg38?

thank you in advance
Forum: Bioinformatics 10-04-2016, 01:39 AM
Replies: 1
Views: 1,364
Posted By edeka
mark duplicates option

Hello. I would like to use MarkDuplicates of Picard, but I don't know how I should use the options. Could anyone give me an example of this .txt file?
Thank you in advance,

best
Forum: Bioinformatics 06-20-2016, 03:34 AM
Replies: 3
Views: 3,532
Posted By edeka
Thank you for your reply. The read is about 20...

Thank you for your reply. The read is about 20 nucleotides, so beedtools should discard this read...
Forum: Literature Watch 06-13-2016, 02:54 AM
Replies: 0
Views: 7,137
Posted By edeka
integrate omics data

Hello!
I am searching papers that reported a good method to integrate omics data (transcriptomic, epigenetic and miRNA) and to create network analysis for autoimmune disease.
Is there anyone who...
Forum: Bioinformatics 06-13-2016, 02:42 AM
Replies: 3
Views: 3,532
Posted By edeka
intersect file bam-bed and count read

Hi all!
I have RNA-seq data and I used STAR in order to align the reads.
I would like to use my bed file in order to have the only read that are mapped in the position reported in bed file and...
Forum: Bioinformatics 05-02-2016, 04:57 AM
Replies: 5
Views: 1,814
Posted By edeka
Thank you (again) for your answer. I am using...

Thank you (again) for your answer. I am using Ribosome profiling data and I need to have the SAM file with the name gene, position on the gene and the sequence.
Forum: Bioinformatics 05-02-2016, 03:27 AM
Replies: 5
Views: 1,814
Posted By edeka
Thank you for your answer. So there isn't a tool...

Thank you for your answer. So there isn't a tool that allow me to convert the output of TopHat directly in order to have the same SAM file but with informations about the gene?
Forum: Bioinformatics 05-02-2016, 02:34 AM
Replies: 5
Views: 1,814
Posted By edeka
tophat gene information

Hi all!
I used tophat2 with the option -G in order to give the gtf file but the output reported the chromosome coordinate. Why? What did I get wrong? How can I obtain the gene information?
Thank...
Forum: Bioinformatics 04-27-2016, 01:34 AM
Replies: 2
Views: 3,254
Posted By edeka
TopHat- index file

Hi all!
I am usign TopHat2 and I get this error:
Beginning TopHat run (v2.0.10)
-----------------------------------------------
Checking for Bowtie
Bowtie 2 not found, checking for older...
Forum: Bioinformatics 04-26-2016, 05:40 AM
Replies: 4
Views: 1,542
Posted By edeka
thank you (again), but I have to download...

thank you (again), but I have to download singularly the sequence?
Forum: Bioinformatics 04-26-2016, 05:18 AM
Replies: 4
Views: 1,542
Posted By edeka
thank you very much. Is there a list for tRNA? ...

thank you very much. Is there a list for tRNA?
Thank you in advance
Forum: Bioinformatics 04-26-2016, 01:45 AM
Replies: 4
Views: 1,542
Posted By edeka
rRNA Yeast

Hi all.
I am searching for complete list of rRNA's sequence of Yeast but I didn't find it. Could anyone help me?

Thank you in advance
Best regards
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