issue with chromosome not found

[manishbiotechie]

hi I am trying to run miRA but I am getting following error 2 lines of the SAM file were ignored because they were invalid The Chromosome was not found as a @SQ entry

test run was successful and i got the desired results. kindly help

[jengelmann]

Hi, thanks for using miRA. The SAM file header needs to have one line for each chromosome or scaffold that appears in your SAM file, e.g. for scaffold_1, this could look like this (SN indicating sequence name and LN sequence length): @SQ SN:scaffold_1 LN:6494944 For a chromosome: @SQ SN:chr_1 LN:8443987 Reads mapped to chromosomes/scaffolds not defined in the header will be ignored. Hope that helps, Julia

[manishbiotechie]

Thanks for your quick response.

@HD VN:1.0 SO:unsorted @SQ SN:Ca_LG_1 LN:39901017 @SQ SN:Ca_LG_2 LN:33233457 @SQ SN:Ca_LG_3 LN:42267542 @SQ SN:Ca_LG_4 LN:54992815 @SQ SN:Ca_LG_5 LN:45819701 @SQ SN:Ca_LG_6 LN:54841389 @SQ SN:Ca_LG_7 LN:45279478 @SQ SN:Ca_LG_8 LN:17664089 @SQ SN:scaffold17332 LN:1136

header of sam file are the above listed ones which appear to be alright, problem is at some point else, kindly help

On Tue, Oct 31, 2017 at 8:15 PM, Julia Engelmann notifications@github.com wrote:

Hi, thanks for using miRA. The SAM file header needs to have one line for each chromosome or scaffold that appears in your SAM file, e.g. for scaffold_1, this could look like this (SN indicating sequence name and LN sequence length): @sq https://github.com/sq SN:scaffold_1 LN:6494944 For a chromosome: @sq https://github.com/sq SN:chr_1 LN:8443987 Reads mapped to chromosomes/scaffolds not defined in the header will be ignored. Hope that helps, Julia

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Manish Tiwari, Pre Doctoral Fellow

National Institute of Plant Genome Research Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi - 110067 , India Mob: +918826766869

[mevers]

Can you double-check that you have matching chromosome names from the BAM and FASTA files? For example, we've come across the situation where reads were aligned against a genome with chromosome names "chr_1", "chr_2", etc. (according to the BAM header), while the reference FASTA file had sequences for chromosomes with names "1", "2", etc. In that case, miRA won't be able to locate the matching chromosome for BAM file-derived expression loci.

[manishbiotechie]

I did checked both files have similar chromosome names

[mevers]

I'm not sure what you mean by "similar chromosome names"; names need to match, i.e. for every name in the BAM file the FASTA files needs to contain sequence with the same name.

I noticed your BAM file is not (position) sorted. Can you re-run miRA using a sorted BAM file, and report if the error persists.