Rsamtools and GenomicAlignments are Bioconductor packages so ask on the
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You cannot rename the seqlevels in the bam file; you could rename the
seqlevels in the object(s) you have created from the bam file.
Martin
On 02/14/2017 09:17 AM, Teresa Tavella wrote:> Dear all,
>
> I would like to ask if it is possible to change the seqnames of a bam file
> giving a vector of character to the function renameSeqlevels. This is
> because in order to use the fuction summarizeOverlap or count/find, the
> seqnames have to match.
>>From the bamfile below I have extracted the locus annotations form the
> seqnames (i.e ERCC00002, NC_001133.9...etc) and I have created a list (same
> length as the seqlevels of the bam file).
>
>
> *bamfile*
> GAlignments object with 6 alignments and 0 metadata columns:
>
> seqnames
>
> <Rle>
> [1]
> DQ459430_gene=ERCC00002_loc:ERCC00002|1-1061|+_exons:1-1061_segs:1-1061
> [2]
> DQ459430_gene=ERCC00002_loc:ERCC00002|1-1061|+_exons:1-1061_segs:1-1061
> [3]
> DQ459430_gene=ERCC00002_loc:ERCC00002|1-1061|+_exons:1-1061_segs:1-1061
> [4]
> DQ459430_gene=ERCC00002_loc:ERCC00002|1-1061|+_exons:1-1061_segs:1-1061
> [5]
> DQ459430_gene=ERCC00002_loc:ERCC00002|1-1061|+_exons:1-1061_segs:1-1061
> [6]
> DQ459430_gene=ERCC00002_loc:ERCC00002|1-1061|+_exons:1-1061_segs:1-1061
> strand cigar qwidth start end width njunc
> <Rle> <character> <integer> <integer>
<integer> <integer> <integer>
> [1] + 8M2D27M 35 1025 1061 37 0
> [2] + 8M2D27M 35 1025 1061 37 0
> [3] - 36M 36 1025 1060 36 0
> [4] - 36M 36 1026 1061 36 0
> [5] + 35M 35 1027 1061 35 0
> [6] + 35M 35 1027 1061 35 0
> -------
> *gffile*
> GRanges object with 6 ranges and 12 metadata columns:
> seqnames ranges strand | source type score
> <Rle> <IRanges> <Rle> |
<factor> <factor> <numeric>
> [1] NC_001133.9 [ 24837, 25070] + | s_cerevisiae exon
<NA>
> [2] NC_001133.9 [ 25048, 25394] + | s_cerevisiae exon
<NA>
> [3] NC_001133.9 [ 27155, 27786] + | s_cerevisiae exon
<NA>
> [4] NC_001133.9 [ 73431, 73792] + | s_cerevisiae exon
<NA>
> [5] NC_001133.9 [165314, 165561] + | s_cerevisiae exon
<NA>
> [6] NC_001133.9 [165388, 165781] + | s_cerevisiae exon
<NA>
> phase gene_id transcript_id exon_number gene_name
> <integer> <character> <character>
<character> <character>
> [1] <NA> XLOC_000040 TCONS_00000191 1 FLO9
> [2] <NA> XLOC_000040 TCONS_00000192 1 FLO9
> [3] <NA> XLOC_000041 TCONS_00000193 1 FLO9
> [4] <NA> XLOC_000055 TCONS_00000200 1 YAL037C-A
> [5] <NA> XLOC_000075 TCONS_00000100 1 YAR010C
> [6] <NA> XLOC_000075 TCONS_00000219 1 YAR010C
> oId nearest_ref class_code
> <character> <character>
<character>
> [1] {TRINITY_GG_normal}16_c1_g1_i1.mrna1 rna8 x
> [2] {TRINITY_GG_normal}16_c0_g1_i1.mrna1 rna8 x
> [3] {TRINITY_GG_normal}12_c0_g1_i1.mrna1 rna8 x
> [4] {TRINITY_GG_normal}3_c3_g1_i1.mrna1 rna31 x
> [5] {TRINITY_GG_normal}3479_c0_g1_i1.mrna1 rna77 x
> [6] {TRINITY_GG_normal}24_c0_g1_i1.mrna1 rna77 x
> tss_id
> <character>
> [1] TSS42
> [2] TSS43
> [3] TSS44
> [4] TSS71
> [5] TSS118
> [6] TSS118
> -------
>
> It is possible to replace the seqlevels names with the list?
> I have tried:
>
> bamfile1 <- renameSeqlevels(seqlevels(bamfile), listx)
>
> Thank you for any advice,
>
> Kind regards,
>
> Teresa
>
>
>
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