User: marina.v.yurieva

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Posts by marina.v.yurieva

<prev • 118 results • page 1 of 12 • next >
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StringTie --merge creates the same id for neighbouring genes
... I'm very sorry if this topic has been posted before, I couldn't find anything relevant. I'm doing assembly with StringTie --merge using reference genome and the list of gtf files from my samples: stringtie --merge -G ref.gtf -o merged.gtf assembly_gtf_list.txt And for many known genes next to ...
ensembl stringtie gene assembly written 14 months ago by marina.v.yurieva520 • updated 6 days ago by kristoffer.vittingseerup3.4k
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Comment: C: Stringtie --merge with PE and SE files
... Most of the data there is PE but there are some samples that are SE. Some of them are even from the same individuals, it's weird. I'm trying to compare tumor to normal tissue from the same individual and there are few of them with PE and SE reads samples as different biological samples. Read lengths ...
written 14 months ago by marina.v.yurieva520
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Stringtie --merge with PE and SE files
... I'm trying to create a merged gtf from TCGA bam files with Stringtie --merge. But some of the files use SE reads and some - PE reads. Are those bam file compatible and can be used together to generate a new gtf? I tried to find this info in the manual and online but couldn't. Thank you! ...
assembly bam written 15 months ago by marina.v.yurieva520
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Comment: C: Gene(s) withTpm value(s) zero in kallisto though reads are mapped
... Does it overlap with another gene on an opposite strand? Maybe the reads are mapped there, not to your gene. Also, you have your gene in the annotation file? Make sure it's not missing. ...
written 2.1 years ago by marina.v.yurieva520
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Comment: C: Stranded RNA-seq data visualization in UCSC
... It's working! Thank you SO much!!! I used bamCoverage from deeptools: bamCoverage -b sample.bam -of bedgraph --filterRNAstrand forward --samFlagExclude 16 --effectiveGenomeSize 2913022398 --normalizeUsing RPKM -o sample_plus.bedGraph I'm not sure if it's enough to just use --filterRNAstrand ...
written 2.1 years ago by marina.v.yurieva520
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Comment: C: bedGraph compress tools
... I tried bamCoverage. It worked really well, only had to play with the bin sizes a few times. Thank you! ...
written 2.1 years ago by marina.v.yurieva520
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Comment: C: Stranded RNA-seq data visualization in UCSC
... Yeah, I looked at everything, just gave the first example. Here is Gapdh: ![enter image description here][1] [1]: https://s8.postimg.cc/vo83t6qpx/strand_error2.png ...
written 2.1 years ago by marina.v.yurieva520
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Comment: C: Stranded RNA-seq data visualization in UCSC
... Thank you! So should I remove the multi-mappers or filter on more specific tags? ...
written 2.1 years ago by marina.v.yurieva520
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Stranded RNA-seq data visualization in UCSC
... I have stranded RNA-seq data which doesn't look stranded when I visualize bedGraphs in Genome Browser: ![enter image description here][1] I tried different aligners (star, bowtie, bwa), different ways to make bedGraph files, nothing works. But when I run salmon on these samples, it detects ISR (pa ...
bedgraph visualization rna-seq stranded written 2.1 years ago by marina.v.yurieva520 • updated 2.1 years ago by Rob4.2k
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Comment: C: Problems uploading custom track to UCSC Genome Browser
... UCSC definitely takes Ensembl IDs but I don't remember if there should be ENSGXXXX.X or it doesn't need ".X" at the end.. ...
written 2.1 years ago by marina.v.yurieva520

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