User: marina.v.yurieva

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Posts by marina.v.yurieva

<prev • 115 results • page 1 of 12 • next >
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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 10 months ago by marina.v.yurieva480
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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 10 months ago by marina.v.yurieva480
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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 10 months ago by marina.v.yurieva480
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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 10 months ago by marina.v.yurieva480
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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 10 months ago by marina.v.yurieva480
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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 10 months ago by marina.v.yurieva480 • updated 10 months ago by Rob3.3k
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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 10 months ago by marina.v.yurieva480
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Comment: C: hg38 gtf file containing all RNAs and features
... If you cannot find all attributes downloading gtf from UCSC try getting it from gencode. If you need some specific features, you can just grep them from gtf making a new file: awk $3=="transcript"{print $0}' if you need the original coordinates from your bed file, try bedtools intersect ...
written 10 months ago by marina.v.yurieva480
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Comment: C: Problems uploading custom track to UCSC Genome Browser
... Does it recognize it as a bed file? (when you upload it go to Manage custom tracks, it should list your file and show file type, number of items in the table. If it doesn't show that file type is "gtf" maybe there is something wrong with formatting. You can check it with vim for tabs etc. It can als ...
written 10 months ago by marina.v.yurieva480
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Comment: C: hg38 gtf file containing all RNAs and features
... Can you show which files you have and what are you trying to get? In general, I wouldn't recommend doing bedtools intersect on a gtf file because bedtools don't really understanf the relations between features like gene -> transcript -> exon and your output file might get very messed up. Defin ...
written 10 months ago by marina.v.yurieva480

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Popular Question 10 months ago, created a question with more than 1,000 views. For Is there an ftp file upload for MG-RAST?
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