User: marina.v.yurieva
marina.v.yurieva • 470
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Posts by marina.v.yurieva
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... 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 6 months ago by
marina.v.yurieva • 470
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... 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 6 months ago by
marina.v.yurieva • 470
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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 6 months ago by
marina.v.yurieva • 470
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... 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 6 months ago by
marina.v.yurieva • 470
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... Thank you! So should I remove the multi-mappers or filter on more specific tags? ...
written 6 months ago by
marina.v.yurieva • 470
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5 follow
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... 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 ...
written 6 months ago by
marina.v.yurieva • 470
• updated
6 months ago by
Rob ♦ 3.1k
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... 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 6 months ago by
marina.v.yurieva • 470
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... 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 6 months ago by
marina.v.yurieva • 470
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... 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 6 months ago by
marina.v.yurieva • 470
0
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... 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 6 months ago by
marina.v.yurieva • 470
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