help to creat bam files from xls sheets

crisant · 04-08-2010, 07:58 PM

Hi, people. I would like to know if there is a basic way to convert excel files (few columns, thousands rows) in bam files. One of the column has short reads (~20nt) that I need to see aligned. Is this possible? Thanks for your time.

PD: I dont have deep knowledge in bioinformatics, so if my problem is hard to solve, please indicate me some references to read.

mgogol · 04-09-2010, 07:10 AM

If you need to align the reads, you need to figure out which aligner to use first, like bowtie or bwa or something.

Then you need to figure out what format file those will take, get your reads into that format, run the aligner, and one of the results will be a bam file.

crisant · 04-09-2010, 10:37 AM

Actually I thought that if I could make a bam file from my xls file, then I could use the Tablet programe. That is the reason why I want to convert to bam. But if I have to use a previous programa (as you said) to the alignement , would I lose the other columns of my xls file? I mean, the ones that have additional information of every read.

mgogol · 04-09-2010, 10:45 AM

On the bedtools mailing list, there was a recent discussion about going from bed (tab-delimited text) to bam. Aaron Quinlan said he might write such software.

I'm not familiar with tablet, but most genome browsers will accept a variety of text based formats, perhaps you could convert your file to one of those other simple formats (bed, gff) or try a different genome browser.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
sorting bam files	frymor	Bioinformatics	23	02-10-2016 06:46 PM
Merging bam files	memento	Bioinformatics	1	02-17-2012 04:39 PM
Reverse engineering BAM files: BAM -> FASTQ	gene coder	Bioinformatics	3	01-03-2012 03:42 PM
NEw to Chip-seq and have .bam/.sam/.bam.bai files... then what?	NGS newbie	Bioinformatics	11	05-25-2011 08:48 AM
Get many Bam Files from 1000genomes	dongshong	Bioinformatics	0	02-20-2011 08:55 PM

04-08-2010, 07:58 PM	#1
crisant Junior Member Location: Rio de Janeiro Join Date: Mar 2010 Posts: 7	help to creat bam files from xls sheets Hi, people. I would like to know if there is a basic way to convert excel files (few columns, thousands rows) in bam files. One of the column has short reads (~20nt) that I need to see aligned. Is this possible? Thanks for your time. PD: I dont have deep knowledge in bioinformatics, so if my problem is hard to solve, please indicate me some references to read.

04-09-2010, 07:10 AM	#2
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	If you need to align the reads, you need to figure out which aligner to use first, like bowtie or bwa or something. Then you need to figure out what format file those will take, get your reads into that format, run the aligner, and one of the results will be a bam file.

04-09-2010, 10:37 AM	#3
crisant Junior Member Location: Rio de Janeiro Join Date: Mar 2010 Posts: 7	Actually I thought that if I could make a bam file from my xls file, then I could use the Tablet programe. That is the reason why I want to convert to bam. But if I have to use a previous programa (as you said) to the alignement , would I lose the other columns of my xls file? I mean, the ones that have additional information of every read.

04-09-2010, 10:45 AM	#4
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	On the bedtools mailing list, there was a recent discussion about going from bed (tab-delimited text) to bam. Aaron Quinlan said he might write such software. I'm not familiar with tablet, but most genome browsers will accept a variety of text based formats, perhaps you could convert your file to one of those other simple formats (bed, gff) or try a different genome browser.