dear all, i am a beginner and i need an information about bam header. The header of my bam file is: @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chrX LN:155270560 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr20 LN:63025520 @SQ SN:chrY LN:59373566 @SQ SN:chr19 LN:59128983 @SQ SN:chr22 LN:51304566 @SQ SN:chr21 LN:48129895 @SQ SN:chr6_ssto_hap7 LN:4928567 @SQ SN:chr6_mcf_hap5 LN:4833398 @SQ SN:chr6_cox_hap2 LN:4795371 @SQ SN:chr6_mann_hap4 LN:4683263 @SQ SN:chr6_apd_hap1 LN:4622290 @SQ SN:chr6_qbl_hap6 LN:4611984 @SQ SN:chr6_dbb_hap3 LN:4610396 @SQ SN:chr17_ctg5_hap1 LN:1680828 @SQ SN:chr4_ctg9_hap1 LN:590426 @SQ SN:chr1_gl000192_random LN:547496 @SQ SN:chrUn_gl000225 LN:211173 @SQ SN:chr4_gl000194_random LN:191469 @SQ SN:chr4_gl000193_random LN:189789 @SQ SN:chr9_gl000200_random LN:187035 @SQ SN:chrUn_gl000222 LN:186861 @SQ SN:chrUn_gl000212 LN:186858 @SQ SN:chr7_gl000195_random LN:182896 @SQ SN:chrUn_gl000223 LN:180455 @SQ SN:chrUn_gl000224 LN:179693 @SQ SN:chrUn_gl000219 LN:179198 @SQ SN:chr17_gl000205_random LN:174588 @SQ SN:chrUn_gl000215 LN:172545 @SQ SN:chrUn_gl000216 LN:172294 @SQ SN:chrUn_gl000217 LN:172149 @SQ SN:chr9_gl000199_random LN:169874 @SQ SN:chrUn_gl000211 LN:166566 @SQ SN:chrUn_gl000213 LN:164239 @SQ SN:chrUn_gl000220 LN:161802 @SQ SN:chrUn_gl000218 LN:161147 @SQ SN:chr19_gl000209_random LN:159169 @SQ SN:chrUn_gl000221 LN:155397 @SQ SN:chrUn_gl000214 LN:137718 @SQ SN:chrUn_gl000228 LN:129120 @SQ SN:chrUn_gl000227 LN:128374 @SQ SN:chr1_gl000191_random LN:106433 @SQ SN:chr19_gl000208_random LN:92689 @SQ SN:chr9_gl000198_random LN:90085 @SQ SN:chr17_gl000204_random LN:81310 @SQ SN:chrUn_gl000233 LN:45941 @SQ SN:chrUn_gl000237 LN:45867 @SQ SN:chrUn_gl000230 LN:43691 @SQ SN:chrUn_gl000242 LN:43523 @SQ SN:chrUn_gl000243 LN:43341 @SQ SN:chrUn_gl000241 LN:42152 @SQ SN:chrUn_gl000236 LN:41934 @SQ SN:chrUn_gl000240 LN:41933 @SQ SN:chr17_gl000206_random LN:41001 @SQ SN:chrUn_gl000232 LN:40652 @SQ SN:chrUn_gl000234 LN:40531 @SQ SN:chr11_gl000202_random LN:40103 @SQ SN:chrUn_gl000238 LN:39939 @SQ SN:chrUn_gl000244 LN:39929 @SQ SN:chrUn_gl000248 LN:39786 @SQ SN:chr8_gl000196_random LN:38914 @SQ SN:chrUn_gl000249 LN:38502 @SQ SN:chrUn_gl000246 LN:38154 @SQ SN:chr17_gl000203_random LN:37498 @SQ SN:chr8_gl000197_random LN:37175 @SQ SN:chrUn_gl000245 LN:36651 @SQ SN:chrUn_gl000247 LN:36422 @SQ SN:chr9_gl000201_random LN:36148 @SQ SN:chrUn_gl000235 LN:34474 @SQ SN:chrUn_gl000239 LN:33824 @SQ SN:chr21_gl000210_random LN:27682 @SQ SN:chrUn_gl000231 LN:27386 @SQ SN:chrUn_gl000229 LN:19913 @SQ SN:chrM LN:16571 @SQ SN:chrUn_gl000226 LN:15008 @SQ SN:chr18_gl000207_random LN:4262 @PG ID:bfast VN:0.6.4e I want to use Dataframe function in this way: DataFrame with 6 rows and 5 columns rname strand pos qwidth <integer> <integer> <integer> <integer> 1 1 1 970 35 2 1 1 971 35 3 1 1 972 35 4 1 1 973 35 5 1 1 974 35 6 1 2 975 35 seq <dnastringset> 1 TATTAGGAAATGCTTTACTGTCATAACTATGAAGA 2 ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG 3 TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA 4 TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC 5 AGGAAATGCTTTACTGTCATAACTATGAAGAGACT 6 GGAAATGCTTTACTGTCATAACTATGAAGAGACTA If i launch: df <- do.call("DataFrame", bam) my result is: DataFrame with 0 rows and 5 columns And my bam file is: $`chr1:1-249250621` $`chr1:1-249250621`$rname factor(0) 93 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chrX chr8 chr9 chr10 ... chr18_gl000207_random $`chr1:1-249250621`$strand factor(0) Levels: + - * $`chr1:1-249250621`$pos integer(0) $`chr1:1-249250621`$qwidth integer(0) $`chr1:1-249250621`$seq A DNAStringSet instance of length 0 $`chr2:1-243199373` $`chr2:1-243199373`$rname factor(0) 93 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chrX chr8 chr9 chr10 ... chr18_gl000207_random $`chr2:1-243199373`$strand factor(0) Levels: + - * $`chr2:1-243199373`$pos integer(0) $`chr2:1-243199373`$qwidth integer(0) $`chr2:1-243199373`$seq A DNAStringSet instance of length 0 What is my error? Where in header BAM file i can find the chr lenghts? Thanks a lot. -- Regards, Capece Vincenzo [[alternative HTML version deleted]]

On 03/29/2011 03:27 AM, Vincenzo Capece wrote: > dear all, > i am a beginner and i need an information about bam header. > The header of my bam file is: > > @SQ SN:chr1 LN:249250621 > @SQ SN:chr2 LN:243199373 > @SQ SN:chr3 LN:198022430 > @SQ SN:chr4 LN:191154276 > @SQ SN:chr5 LN:180915260 > @SQ SN:chr6 LN:171115067 > @SQ SN:chr7 LN:159138663 > @SQ SN:chrX LN:155270560 > @SQ SN:chr8 LN:146364022 > @SQ SN:chr9 LN:141213431 > @SQ SN:chr10 LN:135534747 > @SQ SN:chr11 LN:135006516 > @SQ SN:chr12 LN:133851895 > @SQ SN:chr13 LN:115169878 > @SQ SN:chr14 LN:107349540 > @SQ SN:chr15 LN:102531392 > @SQ SN:chr16 LN:90354753 > @SQ SN:chr17 LN:81195210 > @SQ SN:chr18 LN:78077248 > @SQ SN:chr20 LN:63025520 > @SQ SN:chrY LN:59373566 > @SQ SN:chr19 LN:59128983 > @SQ SN:chr22 LN:51304566 > @SQ SN:chr21 LN:48129895 > @SQ SN:chr6_ssto_hap7 LN:4928567 > @SQ SN:chr6_mcf_hap5 LN:4833398 > @SQ SN:chr6_cox_hap2 LN:4795371 > @SQ SN:chr6_mann_hap4 LN:4683263 > @SQ SN:chr6_apd_hap1 LN:4622290 > @SQ SN:chr6_qbl_hap6 LN:4611984 > @SQ SN:chr6_dbb_hap3 LN:4610396 > @SQ SN:chr17_ctg5_hap1 LN:1680828 > @SQ SN:chr4_ctg9_hap1 LN:590426 > @SQ SN:chr1_gl000192_random LN:547496 > @SQ SN:chrUn_gl000225 LN:211173 > @SQ SN:chr4_gl000194_random LN:191469 > @SQ SN:chr4_gl000193_random LN:189789 > @SQ SN:chr9_gl000200_random LN:187035 > @SQ SN:chrUn_gl000222 LN:186861 > @SQ SN:chrUn_gl000212 LN:186858 > @SQ SN:chr7_gl000195_random LN:182896 > @SQ SN:chrUn_gl000223 LN:180455 > @SQ SN:chrUn_gl000224 LN:179693 > @SQ SN:chrUn_gl000219 LN:179198 > @SQ SN:chr17_gl000205_random LN:174588 > @SQ SN:chrUn_gl000215 LN:172545 > @SQ SN:chrUn_gl000216 LN:172294 > @SQ SN:chrUn_gl000217 LN:172149 > @SQ SN:chr9_gl000199_random LN:169874 > @SQ SN:chrUn_gl000211 LN:166566 > @SQ SN:chrUn_gl000213 LN:164239 > @SQ SN:chrUn_gl000220 LN:161802 > @SQ SN:chrUn_gl000218 LN:161147 > @SQ SN:chr19_gl000209_random LN:159169 > @SQ SN:chrUn_gl000221 LN:155397 > @SQ SN:chrUn_gl000214 LN:137718 > @SQ SN:chrUn_gl000228 LN:129120 > @SQ SN:chrUn_gl000227 LN:128374 > @SQ SN:chr1_gl000191_random LN:106433 > @SQ SN:chr19_gl000208_random LN:92689 > @SQ SN:chr9_gl000198_random LN:90085 > @SQ SN:chr17_gl000204_random LN:81310 > @SQ SN:chrUn_gl000233 LN:45941 > @SQ SN:chrUn_gl000237 LN:45867 > @SQ SN:chrUn_gl000230 LN:43691 > @SQ SN:chrUn_gl000242 LN:43523 > @SQ SN:chrUn_gl000243 LN:43341 > @SQ SN:chrUn_gl000241 LN:42152 > @SQ SN:chrUn_gl000236 LN:41934 > @SQ SN:chrUn_gl000240 LN:41933 > @SQ SN:chr17_gl000206_random LN:41001 > @SQ SN:chrUn_gl000232 LN:40652 > @SQ SN:chrUn_gl000234 LN:40531 > @SQ SN:chr11_gl000202_random LN:40103 > @SQ SN:chrUn_gl000238 LN:39939 > @SQ SN:chrUn_gl000244 LN:39929 > @SQ SN:chrUn_gl000248 LN:39786 > @SQ SN:chr8_gl000196_random LN:38914 > @SQ SN:chrUn_gl000249 LN:38502 > @SQ SN:chrUn_gl000246 LN:38154 > @SQ SN:chr17_gl000203_random LN:37498 > @SQ SN:chr8_gl000197_random LN:37175 > @SQ SN:chrUn_gl000245 LN:36651 > @SQ SN:chrUn_gl000247 LN:36422 > @SQ SN:chr9_gl000201_random LN:36148 > @SQ SN:chrUn_gl000235 LN:34474 > @SQ SN:chrUn_gl000239 LN:33824 > @SQ SN:chr21_gl000210_random LN:27682 > @SQ SN:chrUn_gl000231 LN:27386 > @SQ SN:chrUn_gl000229 LN:19913 > @SQ SN:chrM LN:16571 > @SQ SN:chrUn_gl000226 LN:15008 > @SQ SN:chr18_gl000207_random LN:4262 > @PG ID:bfast VN:0.6.4e > > I want to use Dataframe function in this way: > DataFrame with 6 rows and 5 columns > rname strand pos qwidth > <integer> <integer> <integer> <integer> > 1 1 1 970 35 > 2 1 1 971 35 > 3 1 1 972 35 > 4 1 1 973 35 > 5 1 1 974 35 > 6 1 2 975 35 > seq > <dnastringset> > 1 TATTAGGAAATGCTTTACTGTCATAACTATGAAGA > 2 ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG > 3 TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA > 4 TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC > 5 AGGAAATGCTTTACTGTCATAACTATGAAGAGACT > 6 GGAAATGCTTTACTGTCATAACTATGAAGAGACTA > > If i launch: > df<- do.call("DataFrame", bam) > my result is: > > DataFrame with 0 rows and 5 columns > > And my bam file is: > > $`chr1:1-249250621` > $`chr1:1-249250621`$rname > factor(0) > 93 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chrX chr8 chr9 chr10 ... > chr18_gl000207_random > > $`chr1:1-249250621`$strand > factor(0) > Levels: + - * > > $`chr1:1-249250621`$pos > integer(0) > > $`chr1:1-249250621`$qwidth > integer(0) > > $`chr1:1-249250621`$seq > A DNAStringSet instance of length 0 > > > $`chr2:1-243199373` > $`chr2:1-243199373`$rname > factor(0) > 93 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chrX chr8 chr9 chr10 ... > chr18_gl000207_random > > $`chr2:1-243199373`$strand > factor(0) > Levels: + - * > > $`chr2:1-243199373`$pos > integer(0) > > $`chr2:1-243199373`$qwidth > integer(0) > > $`chr2:1-243199373`$seq > A DNAStringSet instance of length 0 > > What is my error? > Where in header BAM file i can find the chr lenghts? Hi -- after example(scanBam), there is variable 'fl' pointing to a bam file. Let's use that. t = scanBamHeader(fl)[[1]][["targets"]] provides a vector of sequences and lengths from the header file. These are just the values reported in the BAM file; they do not mean that reads from those sequences are present. To find out how many reads are in the file, maybe param = ScanBamParam(which=GRanges(names(t), IRanges(1, t))) countBam(fl, param=param) to query a particular chromosome for the reads, maybe chr = "seq2" param = ScanBamParam( what=c("rname", "strand", "pos", "qwidth", "seq"), which=GRanges(chr, IRanges(1, t[chr]))) bam = scanBam(fl, param=param) DataFrame(bam[[1]]) Martin > > Thanks a lot. > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Hi, On Tue, Mar 29, 2011 at 6:27 AM, Vincenzo Capece <vivo0304 at="" gmail.com=""> wrote: > dear all, > i am a beginner and i need an information about bam header. > The header of my bam file is: [clipped this as its not really important] > > I want to use Dataframe function in this way: > DataFrame with 6 rows and 5 columns > rname strand pos qwidth > <integer> <integer> <integer> <integer> > 1 1 1 970 35 > 2 1 1 971 35 > 3 1 1 972 35 > 4 1 1 973 35 > 5 1 1 974 35 > 6 1 2 975 35 > seq > <dnastringset> > 1 TATTAGGAAATGCTTTACTGTCATAACTATGAAGA > 2 ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG > 3 TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA > 4 TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC > 5 AGGAAATGCTTTACTGTCATAACTATGAAGAGACT > 6 GGAAATGCTTTACTGTCATAACTATGAAGAGACTA > > If i launch: > df <- do.call("DataFrame", bam) How did you get `bam`? This wouldn't work unless `bam` is essentially a list of Vector-like values, and not a list of lists (as is the default that is returned from scaBam. > my result is: > > DataFrame with 0 rows and 5 columns That looks about right: > And my bam file is: > > $`chr1:1-249250621` > $`chr1:1-249250621`$rname > factor(0) > 93 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chrX chr8 chr9 chr10 ... > chr18_gl000207_random > > $`chr1:1-249250621`$strand > factor(0) > Levels: + - * > > $`chr1:1-249250621`$pos > integer(0) > > $`chr1:1-249250621`$qwidth > integer(0) > > $`chr1:1-249250621`$seq > ?A DNAStringSet instance of length 0 > > > $`chr2:1-243199373` > $`chr2:1-243199373`$rname > factor(0) > 93 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chrX chr8 chr9 chr10 ... > chr18_gl000207_random > > $`chr2:1-243199373`$strand > factor(0) > Levels: + - * > > $`chr2:1-243199373`$pos > integer(0) > > $`chr2:1-243199373`$qwidth > integer(0) > > $`chr2:1-243199373`$seq > ?A DNAStringSet instance of length 0 This isn't a "bam file", but rather looks to be a result that was returned by scanBam, but look: the result of your query within the range `chr2:1-243199373` is empty. > What is my error? It seems like a few things, but also hard to diagnose w/o more code from you. The first thing you need to figure out is why your scanBam query isn't returning any reads on chromosome 2. > Where in header BAM file i can find the chr lenghts? You've found it in your header -- sorry I cut it out, but these were the relevant lines: @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 I have a small utility function that reads bam headers and pulls out chromosome info. It uses the `scanBamHeader` function from Rsamtools: parseChromosomeInfoFromBAM <- function(bam.file) { result <- scanBamHeader(bam.file)[[1]]$targets df <- data.frame(name=names(result), length=result) rownames(df) <- NULL df } Which returns a data.frame with the info you're after, like: R> head(parseChromosomeInfoFromBAM('/path/to/file.bam')) name length 1 chr1 249250621 2 chr2 243199373 3 chr3 198022430 4 chr4 191154276 5 chr5 180915260 6 chr6 171115067 Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact