User: snishtala03

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snishtala0340
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Posts by snishtala03

<prev • 30 results • page 1 of 3 • next >
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splicing with UMI barcodes - paired end illumina sequencing
... Hello, I have 250 bps paired end illumina sequencing reads with UMIs. I am interested in identifying splice junctions using my data. I have used STAR in the past for non-UMI runs and was interested in the junctions.out file. Is there a way I can incorporate UMIs into STAR? ( I think right now one ...
illumina umi umitools splicing star written 3 months ago by snishtala0340
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Comment: C: STAR extract reads supporting junction from bam file
... No reason, thanks for pointing that out :) I can make that change. ...
written 7 months ago by snishtala0340
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STAR extract reads supporting junction from bam file
... Hello, I am working with a viral genome and using STAR to find splice junctions. I have 150 bps paired end reads and my reference genotype is ~3500 bps. This is my command - STAR --genomeDir XXX/GenomeInd/ --runThreadN 42 --readFilesIn R1_001.fastq R2_001.fastq --genomeSAindexNbases 5 --sjdb ...
splicing star rna-seq written 7 months ago by snishtala0340
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Comment: C: Significance of column 'strand' and 'max splice overhang' in STAR output
... I did come across that post. It says max splice overhang basically tells the most confident spliced read. I was hoping if I could understand a little more about the importance of this column. I know what a Strand is. I am more interested in knowing why information about a junction from positive or ...
written 8 months ago by snishtala0340
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Significance of column 'strand' and 'max splice overhang' in STAR output
... Hello, I have paired end Illumina data (150 bps). I used STAR and I am interested in identifying novel splice junctions. I am having trouble understanding the significance of 2 columns in the SJ.out.tab file and would really appreciate your help with understanding - What is the need and signific ...
splicing star rna-seq written 8 months ago by snishtala0340 • updated 8 months ago by RamRS30k
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Comment: C: single contig de novo assembly
... Ah, interesting! My host is human. I will try to remove human reads and then try this again. ...
written 10 months ago by snishtala0340
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single contig de novo assembly
... Hello, I am working with RNA-Seq data for a virus. My collaborator gave me a predicted single contig reference which belongs to a particular genotype (let's say GenotypeA) of the virus. Now, some of my samples are from a different genotype (B,C or D) and therefore their mapping % when aligned to my ...
de-novo assembly contig rna-seq written 10 months ago by snishtala0340
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Comment: C: Splicing in virus using long read sequencing
... Since these are PacBio reads the read lengths are variable and MISO cannot handle variable read lengths currently. Can you suggest any other tool or method to do this? ...
written 11 months ago by snishtala0340
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Comment: C: Splicing in virus using long read sequencing
... So my Reference genome is about 3000bp long. It is a predicted reference generated by our team, so we know of a few potential transcripts and exons and their start and end sites but no genes or their locations. MISO needs a gff file. I created a gff with these transcripts and putative splice sites a ...
written 13 months ago by snishtala0340
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Comment: C: Splicing in virus using long read sequencing
... I did but what I am looking for is those plots showing exons and other alternative splicing events and also number of reads supporting it. ...
written 13 months ago by snishtala0340

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Popular Question 10 months ago, created a question with more than 1,000 views. For GAGE or GSEABase using expression data and pathway.gmt file for mouse
Popular Question 3.0 years ago, created a question with more than 1,000 views. For GAGE or GSEABase using expression data and pathway.gmt file for mouse

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