Question: RNA Seq Workflow
1
gravatar for jadepinket
21 months ago by
jadepinket10
jadepinket10 wrote:

I am using the RNA-seq workflow: gene-level exploratory analysis and differential expression. I have summerizeoverlap output 0

so <- summarizeOverlaps(ebg, "Epigenomics02-96.alignments.bam", mode="Union",
+                         singleEnd=FALSE,
+                         ignore.strand=TRUE,
+                         fragments=TRUE )
There were 26 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

input files Homo_sapiens.GRCh38.89.gtf 02-96.alignments.bam Do I need to sort the bam file Here is how it looks

NB501343:44:HNMWTBGXY:3:21409:23096:14722       0       chrM    713     50      25M1D49M        *       0       0   EEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE/E       AS:i:-8 XM:i:0  XO:i:1  XG:i:1  MD:Z:25^C49     NM:i:1  NH:i:1  XS:A:-  RG:Z
NB501343:44:HNMWTBGXY:1:13201:1233:3457 0       chrM    924     50      24M1I47M        *       0       0       CAATE6EEEEE6EEEE//EEEEEEEEE AS:i:-8 XM:i:0  XO:i:1  XG:i:1  MD:Z:71 NM:i:1  NH:i:1  XS:A:-  RG:Z:0
NB501343:44:HNMWTBGXY:1:13202:26691:3452        0       chrM    924     50      24M1I47M        *       0       0   EEEEEEEEEEEEEEEEEAEE/AAEEEAEEEE AS:i:-8 XM:i:0  XO:i:1  XG:i:1  MD:Z:71 NM:i:1  NH:i:1  XS:A:-  RG:Z:0

Thanks in advance

rna-seq gene • 856 views
ADD COMMENTlink modified 21 months ago by ptinto190 • written 21 months ago by jadepinket10

The 2 combined objects have no sequence levels in common.

ADD REPLYlink written 21 months ago by cpad011211k

Thanks Devon, I am getting the GTF file from UCSC, I have chosen track: ALL GENCODE V26. Does that seem correct?

ADD REPLYlink written 21 months ago by jadepinket10
1

[polite advice] @jadepinket, this is not an answer but a comment, so you should add it as a comment under Devon's answer.

ADD REPLYlink written 21 months ago by ptinto190

Post the first few lines of your GTF file, my guess is that somehow you have chromosome names like 1 and MT.

ADD REPLYlink written 21 months ago by Devon Ryan89k
4
gravatar for ptinto
21 months ago by
ptinto190
ptinto190 wrote:

This seems a classic clash between Ensembl and UCSC coordinates.

I don't know how you have downloaded your gtf file from ucsc, but the "89" part, is the typical notation for Ensembl version Homo_sapiens.GRCh38.89.gtf. Indeed you can download this file from Ensembl here ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/

UCSC has all chromosome name starting with "chr" and ensembl have only the number. Also the mitochondrial genome in UCSC is chrM and in Ensembl is MT. So your coordinate names from both files are totally different

ADD COMMENTlink modified 21 months ago • written 21 months ago by ptinto190
3
gravatar for Devon Ryan
21 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Your BAM file uses UCSC chromosome names, your GTF file doesn't.

ADD COMMENTlink written 21 months ago by Devon Ryan89k
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