Question: (Closed) picard. Cannot add sequence that already exists in SAMSequenceDictionary
0
gravatar for flyingfrogiching
3.1 years ago by
Taiwan
flyingfrogiching0 wrote:

 

i have several questions and how someone could answer me

 


I am just learning how to analyse data

this is my steps

1. download library, combine them into single csv file by CRISPR.sgRNA_create_ref_fasta

2. bowtie2 apple$ ./bowtie2-build CL.fa CrL

3.Billyde-MacBook:bowtie2 apple$ ./bowtie2 -x CrL -U -f R.fa  -S 


4Picard Sortsam
->  apple$ java -Xmx2g -jar picard.jar SortSam INPUT=test OUTPUT=result.sam SORT_ORDER=queryname 

but error-> Cannot add sequence that already exists in SAMSequenceDictionary: A1BG


- - -
with:
./samtools view -H R
[W::sam_hdr_parse] duplicated sequence 'A1BG'
[W::sam_hdr_parse] duplicated sequence 'A1BG'
[W::sam_hdr_parse] duplicated sequence 'A1CF'
[W::sam_hdr_parse] duplicated sequence 'A1CF'
[W::sam_hdr_parse] duplicated sequence 'A2M'
[W::sam_hdr_parse] duplicated sequence 'A2M'
[W::sam_hdr_parse] duplicated sequence 'A2ML1'
[W::sam_hdr_parse] duplicated sequence 'A2ML1'
[W::sam_hdr_parse] duplicated sequence 'A3GALT2'
[W::sam_hdr_parse] duplicated sequence 'A3GALT2'
... and many


- -

do there have any idea why " Cannot add sequence that already exists in SAMSequenceDictionary: A1BG"

I have tried many different way to fit it but still not work 

I have also try 
samtools rmdup <input.bam> <output.bam>
or
samtools rmdup -s <input.bam> <output.bam>

butnotthing help

 

-

 

 

 

bowtie samtools • 1.1k views
ADD COMMENTlink modified 3.1 years ago by Martin Čech ♦♦ 4.6k • written 3.1 years ago by flyingfrogiching0

Hello flyingfrogiching!

We believe that this post is does not fit the main topic of this site.

This forum is dedicated to the usage of Galaxy (http://usegalaxy.org).

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.1 years ago by Jennifer Hillman Jackson25k
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