Hi! I hope you're doing great.
I'm opening this issue regarding a JCounts Error when analyzing BAM files of S. lycopersicum data. Here's the error:
BAMFiles <- c("Control_1.bam","Control_2.bam", "Control_3.bam", "NaCl_1h_1.bam", "NaCl_1h_2.bam", "NaCl_1h_3.bam")
targets <- data.frame(row.names = paste0('Sample',c(1:6)),
-
-
f1 = c( 'control','control','control','treatment','treatment', 'treatment'),
-
stringsAsFactors = FALSE); targets
bam f1
Sample1 Control_1.bam control
Sample2 Control_2.bam control
Sample3 Control_3.bam control
Sample4 NaCl_1h_1.bam treatment
Sample5 NaCl_1h_2.bam treatment
Sample6 NaCl_1h_3.bam treatment
mBAMs <- data.frame( bam = c("Control_sorted.bam", "NaCl_1h_sorted.bam"),
-
condition = c("control","treatment")); mBAMs
bam condition
1 Control_sorted.bam control
2 NaCl_1h_sorted.bam treatment
gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 18, maxISize = 50000, libType="PE", strandMode=0)
Summarizing Sample1
ETA: 43 min
Summarizing Sample2
ETA: 35 min
Summarizing Sample3
ETA: 26 min
Summarizing Sample4
ETA: 20 min
Summarizing Sample5
ETA: 11 min
Summarizing Sample6
ETA: 0 min
There were 12 warnings (use warnings() to see them)
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="PE", strandMode=0) #unstranded
Junctions PJU completed
Error in .local(x, use.names, use.mcols, ...) :
For some pairs in 'x', the 2 alignments are not on the same chromosome.
Cannot associate a unique genomic range to such pairs. Please call
granges() with 'on.discordant.seqnames="drop"' to drop these pairs, or
with 'on.discordant.seqnames="split"' to represent each of them with 2
genomic ranges in the returned GRanges object. Note that in both cases
the returned object won't be parallel to 'x'. Alternatively, please
consider using grglist() instead of granges() to turn 'x' into a
GRangesList object instead of a GRanges object. See ?GAlignmentPairs
for more information.
In addition: Warning messages:
1: In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, :
24899 alignments with ambiguous pairing were dumped.
Use 'getDumpedAlignments()' to retrieve them from the dump environment.
2: In FUN(X[[i]], ...) :
Some seqnames had a '.' present in their names. ASpli had to normalize them using '_'.
I read that you can either treat the data as SE (and I'm not sure which would be the implications, whether I should or not do it with my data) or that I could try to remove/drop these in the alignment step (I use Hisat, and I'm not sure how to drop it). Can you give me any insight on this issue? Or any advice?
Thanks a lot in advance!!
My session info, just in case:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.3
Hi! I hope you're doing great.
I'm opening this issue regarding a JCounts Error when analyzing BAM files of S. lycopersicum data. Here's the error:
BAMFiles <- c("Control_1.bam","Control_2.bam", "Control_3.bam", "NaCl_1h_1.bam", "NaCl_1h_2.bam", "NaCl_1h_3.bam")
targets <- data.frame(row.names = paste0('Sample',c(1:6)),
Sample1 Control_1.bam control
Sample2 Control_2.bam control
Sample3 Control_3.bam control
Sample4 NaCl_1h_1.bam treatment
Sample5 NaCl_1h_2.bam treatment
Sample6 NaCl_1h_3.bam treatment
mBAMs <- data.frame( bam = c("Control_sorted.bam", "NaCl_1h_sorted.bam"),
1 Control_sorted.bam control
2 NaCl_1h_sorted.bam treatment
gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 18, maxISize = 50000, libType="PE", strandMode=0)
Summarizing Sample1
ETA: 43 min
Summarizing Sample2
ETA: 35 min
Summarizing Sample3
ETA: 26 min
Summarizing Sample4
ETA: 20 min
Summarizing Sample5
ETA: 11 min
Summarizing Sample6
ETA: 0 min
There were 12 warnings (use warnings() to see them)
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="PE", strandMode=0) #unstranded
Junctions PJU completed
Error in .local(x, use.names, use.mcols, ...) :
For some pairs in 'x', the 2 alignments are not on the same chromosome.
Cannot associate a unique genomic range to such pairs. Please call
granges() with 'on.discordant.seqnames="drop"' to drop these pairs, or
with 'on.discordant.seqnames="split"' to represent each of them with 2
genomic ranges in the returned GRanges object. Note that in both cases
the returned object won't be parallel to 'x'. Alternatively, please
consider using grglist() instead of granges() to turn 'x' into a
GRangesList object instead of a GRanges object. See ?GAlignmentPairs
for more information.
In addition: Warning messages:
1: In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, :
24899 alignments with ambiguous pairing were dumped.
Use 'getDumpedAlignments()' to retrieve them from the dump environment.
2: In FUN(X[[i]], ...) :
Some seqnames had a '.' present in their names. ASpli had to normalize them using '_'.
I read that you can either treat the data as SE (and I'm not sure which would be the implications, whether I should or not do it with my data) or that I could try to remove/drop these in the alignment step (I use Hisat, and I'm not sure how to drop it). Can you give me any insight on this issue? Or any advice?
Thanks a lot in advance!!
My session info, just in case:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.3