Upload Bam file to custom track UCSC Genome Browser

gabrielw · 06-02-2011, 11:01 AM

I 'm a newbie in mapping stuff, so I'm training mapping 454 reads, first of all I mapped one file that I got in sra database... so I mapped it using bwa, genereted an sam file... I converted to bam....

but when I try to upload to http://genome.ucsc.edu/cgi-bin/hgCustom , using the browser to upload directly from my PC and click "submit", it says that Can't read file.bam !!!
Can someone help me ?? I know that there is other way to upload , hosting the file into a link... but I don 't have where to host my file.bam

dawe · 06-02-2011, 01:13 PM

You don't have to upload a bam file. You need to have it visible at a certain ftp or http uri, then add

track type=bam bigDataUrl=http://link/to/your/bam/file

just be sure you have indexed the bam file.

d

ulz_peter · 06-02-2011, 11:07 PM

Just in case your BAM file is too large, you could split it and index the splitted parts.

In case your BAM File is broken: you could check that out using the picard validateSamFile option.

But in any case: uploading a large BAM file is slow and loading the data over an external http/ftp server certainly would be a good idea. If you only plan to visualize your alignments you could use stanalone visualization prgrams like IGV, Savant or different others. They also can visualize accompanying data if you got them in the right data format. That would save you some time and issues of uploading...

sdarko · 06-03-2011, 06:22 AM

I will second the use of IGV from Broad. It's a great tool to locally view alignments.

http://www.broadinstitute.org/igv/

gabrielw · 06-15-2011, 12:26 PM

sorry for the late answer!
thanks all for your help... I used picard to validatesam to my bam file and thats what happened
ERROR: Read groups is empty
WARNING: Record 1, Read name SRR013983.23952, NM tag (nucleotide differences) is missing
WARNING: Record 2, Read name SRR013983.59880, NM tag (nucleotide differences) is missing
WARNING: Record 3, Read name SRR013983.22265, NM tag (nucleotide differences) is missing

and etc.....

do u know what is happening? thnks

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06-02-2011, 11:01 AM	#1
gabrielw Junior Member Location: Brazil Join Date: Dec 2010 Posts: 3	Upload Bam file to custom track UCSC Genome Browser I 'm a newbie in mapping stuff, so I'm training mapping 454 reads, first of all I mapped one file that I got in sra database... so I mapped it using bwa, genereted an sam file... I converted to bam.... but when I try to upload to http://genome.ucsc.edu/cgi-bin/hgCustom , using the browser to upload directly from my PC and click "submit", it says that Can't read file.bam !!! Can someone help me ?? I know that there is other way to upload , hosting the file into a link... but I don 't have where to host my file.bam

06-02-2011, 01:13 PM	#2
dawe Senior Member Location: 45°30'25.22"N / 9°15'53.00"E Join Date: Apr 2009 Posts: 258	You don't have to upload a bam file. You need to have it visible at a certain ftp or http uri, then add track type=bam bigDataUrl=http://link/to/your/bam/file just be sure you have indexed the bam file. d

06-02-2011, 11:07 PM	#3
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	Just in case your BAM file is too large, you could split it and index the splitted parts. In case your BAM File is broken: you could check that out using the picard validateSamFile option. But in any case: uploading a large BAM file is slow and loading the data over an external http/ftp server certainly would be a good idea. If you only plan to visualize your alignments you could use stanalone visualization prgrams like IGV, Savant or different others. They also can visualize accompanying data if you got them in the right data format. That would save you some time and issues of uploading...

06-03-2011, 06:22 AM	#4
sdarko Member Location: Bethesda, MD Join Date: Apr 2009 Posts: 51	I will second the use of IGV from Broad. It's a great tool to locally view alignments. http://www.broadinstitute.org/igv/

06-15-2011, 12:26 PM	#5
gabrielw Junior Member Location: Brazil Join Date: Dec 2010 Posts: 3	sorry for the late answer! thanks all for your help... I used picard to validatesam to my bam file and thats what happened ERROR: Read groups is empty WARNING: Record 1, Read name SRR013983.23952, NM tag (nucleotide differences) is missing WARNING: Record 2, Read name SRR013983.59880, NM tag (nucleotide differences) is missing WARNING: Record 3, Read name SRR013983.22265, NM tag (nucleotide differences) is missing and etc..... do u know what is happening? thnks