User: Lalla

gravatar for Lalla
Lalla40
Reputation:
40
Status:
New User
Location:
Germany
Last seen:
3 days, 16 hours ago
Joined:
4 years, 2 months ago
Email:
a**********@gmail.com

Posts by Lalla

<prev • 23 results • page 1 of 3 • next >
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Retrieve PTM (protein post translational modifications) for a list of protein coordinates (specific exons)
... Dear all I am analyzing a set of alternative spliced, protein-coding, exons. I have been able to map the exons coordinates to the corresponding protein coordinates and find domains annotated for those positions. Another question I would like to address is whether those spliced exons encode for prot ...
ptm splicing proteins written 4 weeks ago by Lalla40
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Alt Analyze: problem with calls of events
... Dear all, I am trying several tools to analyze alternative splicing. one of the most promising and reported to be very accurate is AltAnalyze. The interface is extremely user friendly and does not require coding skills. The output covers almost everything one could imagine: splicing events, associa ...
altanalyze splicing tools alternative splicing written 22 months ago by Lalla40 • updated 22 months ago by Nathan Salomonis40
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Comment: A: Paired end sequencing with different read length: better to trim everything to a
... Ok, I will try both ways then. Thanks for the suggestions! ...
written 22 months ago by Lalla40
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Comment: C: Paired end sequencing with different read length: better to trim everything to a
... Dear genomax thank you for your reply. Unfortunately I do not know. I am not a bioinformatician, and the quality trimming, mapping and alignment has been done by our in house bioinformaticians. We work on mouse, so I believe that if they decided to trim those reads it was for a good reason and I wo ...
written 22 months ago by Lalla40
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Paired end sequencing with different read length: better to trim everything to a short length or use long single end
... Dear all, I am working on alternative splicing. I have paired-end sequencing data of different length (100 bp for the forward and 66 for the reverse, trimmed because of low quality). My problem is that some tools for alternative splicing, such as MISO or rMATS, require reads of the same length. I c ...
alternative splicing rna-seq read length written 22 months ago by Lalla40 • updated 5 months ago by iti.gupta0
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Answer: A: Isoform switch, definition and selection of candidates
... Hi! Another question. Does this tool give the genomic coordinates of the spliced exon? Thanks a lot! ...
written 2.1 years ago by Lalla40
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Answer: A: Isoform switch, definition and selection of candidates
... Hi Kristoffer! Thanks a lot! I went ahead with my analysis but I feel it is incomplete and I would like to add more information. The tool you report seems to help a lot in the analysis of isoform switching. Does it also support data from Ballgown? I gave a try to this tool because it claimed to b ...
written 2.1 years ago by Lalla40
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Comment: A: determining isoform usage with Jensen-Shannon metric and eXpress output
... Hi sah9b! I am currently attempting to do the same. In my case I would like to try to apply the JSD on the transcripts reconstructed with Ballgown (and then try to apply the same logic to the exons, but I am not sure if this is really correct). Did you find the solution? How did it work? Would you ...
written 2.3 years ago by Lalla40
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Ensembl retired transcript IDs
... Hi! I have some transcript IDs mapped with Ensembl 67. I want to study the corresponding proteins but some of the IDs are not present in the newest Ensembl release and Protein databases are usually updated to the most recent annotations (or previous annotation but anyway more recent than the 67). M ...
archive ensembl id history converter written 4.0 years ago by Lalla40 • updated 3.9 years ago by Biostar ♦♦ 20
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Isoform switch, definition and selection of candidates
... Hi! I'm dealing with alternative splicing and isoform switching. I am trying to find interesting candidates for my research from a transcriptome analysis. We run Cufflinks/Cuffdiff2 to estimate differential expression of genes, isoforms, cds (coding sequence). For what I understand in an alternati ...
isoform switch cuffdiff alternative splicing written 4.1 years ago by Lalla40

Latest awards to Lalla

Popular Question 20 months ago, created a question with more than 1,000 views. For Ensembl retired transcript IDs
Popular Question 20 months ago, created a question with more than 1,000 views. For Isoform switch, definition and selection of candidates
Popular Question 20 months ago, created a question with more than 1,000 views. For Protein ID and Protein domain ID description
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Protein ID and Protein domain ID description
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Isoform switch, definition and selection of candidates
Student 4.0 years ago, asked a question with at least 3 up-votes. For Retrieve protein domain coordinates given a protein/transcript ID

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