hot to view alihment when there are more than 100 refrence files

[DHWANI DHOLAKIA]

i have a sorted bam and .bai file . but the reference file is a collection of all possible HLA alleles in HLA database . In such situation when there is not a single reference like as in case of hg19 or human genome file, how to visualise the alignments.

[DHWANI DHOLAKIA]

when i try to load the bam file it shows this error

An error occurred while accessing: /home/dhwani/Desktop/Sample_AyuPC142a_exon23_high_resolution_multi_ref_mappedreads_sorted_puri_mappedreads_sorted.bam Fasta file has uneven line lengths in contig null

[DHWANI DHOLAKIA]

i am sorry there is a typo in the following line

how to view alignment when there are more than 100 refrence files

[Jim Robinson]

You'll have to do 2 things to load this reference (1) concatenate all the individual fasta files into a single file,  (2) fix the line lengths so  that each line  has the same number of characters except the last line of each sequence.  This does not include the sequence name line (the lines that start with ">").

On 11/15/15 11:17 PM, DHWANI DHOLAKIA wrote:

when i try to load the bam file it shows this error

An error occurred while accessing: /home/dhwani/Desktop/Sample_AyuPC142a_exon23_high_resolution_multi_ref_mappedreads_sorted_puri_mappedreads_sorted.bam Fasta file has uneven line lengths in contig null

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[DHWANI DHOLAKIA]

My file is already concatenated. but it becomes very difficult to match 100 files individually. What is the best possible in such situtation to view files

[Jim Robinson]

Hi,  I think I answered your question already, you might have to write a script to prepare the fasta file.    Google "index fasta file samtools"  for more details.

Jim

On 11/16/15 7:46 AM, DHWANI DHOLAKIA wrote:

My file is already concatenated. but it becomes very difficult to match 100 files individually. What is the best possible in such situtation to view files

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