User: MarVi

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MarVi20
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Posts by MarVi

<prev • 29 results • page 1 of 3 • next >
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Quicker way to know if a SNV is involved in a mismatch alignment
... Dear all, I have an advice to ask. I have a collection of alignments, of which I want to know if the mismatches found in the reads when comparing with the reference sequence (genome) are due to an SNV. I have all the SNV's noted down and stored per chromosome in python dictionaries. However, the pr ...
cpickle python mismatch alignment dictionary written 14 days ago by MarVi20 • updated 14 days ago by JC12k
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Comment: C: Preventing alignment to new Splice Junctions with STAR
... Thanks so much! You were of much help! ...
written 14 days ago by MarVi20
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Preventing alignment to new Splice Junctions with STAR
... Hello to all, I hope everyone is well! I want to ask if anyone knows if there are any parameters in STAR that prevent the alignment of reads to unannotated splice junctions? I want to speed the alignment task by limiting alignments to splice junctions that are not known. I already included --sjdbSc ...
splice-junctions alignment sequence star written 15 days ago by MarVi20 • updated 15 days ago by benformatics2.0k
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Comment: C: Why STAR Aligner limits alignments to soft-masked regions (lowercase letters in
... Thanks for you reply ! So, in conclusion, STAR isn't a good aligner to align reads to repetitive regions! I didn't find any explanation of why this happens. I made some tests with Hard and Soft masked reference and actually, the result was the same. It seems that STAR simply doesn't align to repet ...
written 10 weeks ago by MarVi20
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Why STAR Aligner limits alignments to soft-masked regions (lowercase letters in reference genome)?
... Hello All, I have been trying to figure out what would be the best parameters to use in the STAR aligner to find all possible alignments to an rna read. I realized that somehow STAR limits alignments or does not find a way to do alignments in soft mask regions. As I tried GSNAP and with this alig ...
alignment soft-masked regions genome gsnap written 11 weeks ago by MarVi20 • updated 4 weeks ago by Devon Ryan97k
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Comment: C: Annotation Human genome transcripts, Transcript Support Level meaning
... Thank you very much for your kind response! I have been revising the literature that you cited here, and it is very useful! However, I still have a question, why there are some transcripts that are pseudogenes but are assigned to a TSL different from "NA"? ...
written 15 months ago by MarVi20
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Annotation Human genome transcripts, Transcript Support Level meaning
... Dear all, I have som few questions related to the annotation of non-coding transcripts. Hopefully, someone here knows some or all the answers. Does someone know what does it mean the **Transcript support level: NA** in some of the transcripts in the Gencode/Ensembl annotation gtf? In their web sit ...
gene annotation transcripts ensembl written 15 months ago by MarVi20 • updated 15 months ago by Emily_Ensembl21k
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Comment: C: Cufflinks merge not report Transcripts?
... Hi Vijay, Thank you very much for your nice response and advice! Actually, I have been using both StringTie and Cufflinks for transcriptome reconstruction, (Alignments are made with STAR.) Then, I have noticed that StringTie is quite fast compared to Cufflinks and it reports 'fairly' enough number ...
written 23 months ago by MarVi20
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Cufflinks merge not report Transcripts?
... Hello everyone, I modify the question. It still being related to Cufflinks. Does someone know why when cufflinks merge is used, only the exons are reported? Why the transcripts are not associated? As on the output of cufflinks algorithm. CuffMerge GL000205.2 Cufflinks exon 54409 56709 . - . ...
cufflinks rna-seq written 23 months ago by MarVi20
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Comment: C: How to efficiently remove a list of reads according to their ID and mapped posit
... My example is not a real example and not always are the two first. Removal is based in their positions (chr:start-end). ...
written 2.3 years ago by MarVi20

Latest awards to MarVi

Popular Question 15 months ago, created a question with more than 1,000 views. For Understanding MAPping Quality in SAM file / Star
Popular Question 22 months ago, created a question with more than 1,000 views. For Understanding MAPping Quality in SAM file / Star
Popular Question 22 months ago, created a question with more than 1,000 views. For Export coverage Track from IGV

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