@mastal511 I have the [bam.bai] file in the same folder as the bam file. Is that what I have to do? How do I sort the bam file?
I loaded a BAM file in IGV but I can't see anything. My reference genome is Human hg19. I don't know which chromosome to choose and which region to zoom in.
I tried to read the BAM file header with samtools but I don't understand what information to extract:
I wrote that in the terminal
samtools view -h [bamfile] | head -100
OUTPUT
aln.bam | head -88
@HD VN:1.0 SO:unsorted
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663
@SQ SN:8 LN:146364022
@SQ SN:9 LN:141213431
@SQ SN:10 LN:135534747
@SQ SN:11 LN:135006516
@SQ SN:12 LN:133851895
@SQ SN:13 LN:115169878
@SQ SN:14 LN:107349540
@SQ SN:15 LN:102531392
@SQ SN:16 LN:90354753
@SQ SN:17 LN:81195210
@SQ SN:18 LN:78077248
@SQ SN:19 LN:59128983
@SQ SN:20 LN:63025520
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:X LN:155270560
@SQ SN:Y LN:59373566
@SQ SN:MT LN:16569
@SQ SN:GL000207.1 LN:4262
@SQ SN:GL000226.1 LN:15008
@SQ SN:GL000229.1 LN:19913
@SQ SN:GL000231.1 LN:27386
@SQ SN:GL000210.1 LN:27682
@SQ SN:GL000239.1 LN:33824
@SQ SN:GL000235.1 LN:34474
@SQ SN:GL000201.1 LN:36148
@SQ SN:GL000247.1 LN:36422
@SQ SN:GL000245.1 LN:36651
@SQ SN:GL000197.1 LN:37175
@SQ SN:GL000203.1 LN:37498
@SQ SN:GL000246.1 LN:38154
@SQ SN:GL000249.1 LN:38502
@SQ SN:GL000196.1 LN:38914
@SQ SN:GL000248.1 LN:39786
@SQ SN:GL000244.1 LN:39929
@SQ SN:GL000238.1 LN:39939
@SQ SN:GL000202.1 LN:40103
@SQ SN:GL000234.1 LN:40531
@SQ SN:GL000232.1 LN:40652
@SQ SN:GL000206.1 LN:41001
@SQ SN:GL000240.1 LN:41933
@SQ SN:GL000236.1 LN:41934
@SQ SN:GL000241.1 LN:42152
@SQ SN:GL000243.1 LN:43341
@SQ SN:GL000242.1 LN:43523
@SQ SN:GL000230.1 LN:43691
@SQ SN:GL000237.1 LN:45867
@SQ SN:GL000233.1 LN:45941
@SQ SN:GL000204.1 LN:81310
@SQ SN:GL000198.1 LN:90085
@SQ SN:GL000208.1 LN:92689
@SQ SN:GL000191.1 LN:106433
@SQ SN:GL000227.1 LN:128374
@SQ SN:GL000228.1 LN:129120
@SQ SN:GL000214.1 LN:137718
@SQ SN:GL000221.1 LN:155397
@SQ SN:GL000209.1 LN:159169
@SQ SN:GL000218.1 LN:161147
@SQ SN:GL000220.1 LN:161802
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000211.1 LN:166566
@SQ SN:GL000199.1 LN:169874
@SQ SN:GL000217.1 LN:172149
@SQ SN:GL000216.1 LN:172294
@SQ SN:GL000215.1 LN:172545
@SQ SN:GL000205.1 LN:174588
@SQ SN:GL000219.1 LN:179198
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000223.1 LN:180455
@SQ SN:GL000195.1 LN:182896
@SQ SN:GL000212.1 LN:186858
@SQ SN:GL000222.1 LN:186861
@SQ SN:GL000200.1 LN:187035
@SQ SN:GL000193.1 LN:189789
@SQ SN:GL000194.1 LN:191469
@SQ SN:GL000225.1 LN:211173
@SQ SN:GL000192.1 LN:547496
@RG ID:Bordet_EGFR_S1 SM:S1 PL:Illumina
@PG ID:bowtie2 PN:bowtie2 VN:2.0.2
M01636:3:000000000-A442D:1:1102:18789:14479 99 1 326181 1 11S140M = 326217 189 CACACTGACGTGCCTCTCCAGACCCACTTGCACCCTCCGGGCGTTCTCTCCGGGCCCAGCTCTTCTTCCTGGTTGGGTCTCCAGGCCCGATTCCTGCCTCTCAACAACCTCTTTGGACTCAGTGCCTACCCATCTCCTGGCGGCCTTGGTC BBBBBFFFFBBAEGGGGGGGGGGHHHCFHHHGHHGHGGGGGGGGCFFHHHHGGGGEGDHHGFGG3FGHHHFEGHEGGGGHHFHHGEFFGGGGH4FGEGFFHGHFGHFHGHHHFHGHHGHHHFBHHFHBHHGHHHHHFFFHG-CGGDGFHHB AS:i:280 XS:i:280 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:140 YS:i:275 YT:Z:CP RG:Z:Bordet_EGFR_S1
How to find the correct chromosome and the region of interest?
Thanks
3 answers
I think you need to sort and index the bam file using samtools before you can see anything in IGV.
Did you sort the BAM file before indexing it (which creates the .bai file)?
Actually my instructor sent me 4 files:
- aln1.fastq
- aln2.fastq
- aln.bam
- aln.bam.bai
That's why I was thinking that it was already sorted. As genomax2 said it's maybe because my reference genome is not hg19. How can I set it as reference in samtools?
In addition to @mastal511's suggestion it looks like you have "ensembl" version of the genome/annotation where as the default "genome" in IGV is UCSC (which uses chr1 etc). So you may need to load the ensembl version of hg19 in IGV as a "new genome".
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