I am trying to select some reference genome region of a bam file, but got an error

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3.7 years ago

schlogl ▴ 160

Hi there, I am trying to use this command:

samtools view -b sorted_SRR1972739.bwa.bam AF086833:3050-3199 > selected.bam

And got this error:

[main_samview] region "AF086833:3050" specifies an unknown reference name. Continue anyway.

Using this command:

samtools view -c selected.bam
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The file I used as ref genoma was AF086833 (AF086833.2 Ebola virus - Mayinga, Zaire, 1976, complete genome).

All the anterior commands worked well and were:

bwa mem AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq  > SRR1972739.bwa.sam
samtools view -S -b SRR1972739.bwa.sam > SRR1972739.bwa.bam
samtools sort SRR1972739.bwa.bam -o sorted_SRR1972739.bwa.bam
samtools index sorted_SRR1972739.bwa.bam

Do you have any ideia what I am doing wrong to get this error.

Thank you,

Paulo.

SAMTOOLS • 1.5k views

ADD COMMENT • link updated 3.7 years ago by lieven.sterck 15k • written 3.7 years ago by schlogl ▴ 160

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no need to shout (== caps in the title, I changed it for you this time)

ADD REPLY • link 3.7 years ago by lieven.sterck 15k

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sorry. Thank you. Paulo

ADD REPLY • link 3.7 years ago by schlogl ▴ 160

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did you double check the correct syntax for querying a specific region?

ADD REPLY • link 3.7 years ago by lieven.sterck 15k

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Yep! Look here http://www.htslib.org/doc/samtools-view.html[1]

ADD REPLY • link updated 3.7 years ago by lieven.sterck 15k • written 3.7 years ago by schlogl ▴ 160

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can you post the first line of the fasta file you're using? (= the header line)

ADD REPLY • link 3.7 years ago by lieven.sterck 15k

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AF086833.2 Ebola virus - Mayinga, Zaire, 1976, complete genome

ADD REPLY • link 3.7 years ago by schlogl ▴ 160

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as you figured out by now, you were not using the correct sequence name ;)

ADD REPLY • link 3.7 years ago by lieven.sterck 15k

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What's the output of samtools idxstats sorted_SRR1972739.bwa.bam?

By the way, your command could be a lot shorter, avoiding unnecessary intermediate files. This assumes you are using a fairly recent version of samtools, but you should make sure to work with up-to-date tools anyway.

You can replace the following

bwa mem AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq  > SRR1972739.bwa.sam
samtools view -S -b SRR1972739.bwa.sam > SRR1972739.bwa.bam
samtools sort SRR1972739.bwa.bam -o sorted_SRR1972739.bwa.bam

by

bwa mem AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq  | samtools sort -o sorted_SRR1972739.bwa.bam

ADD REPLY • link 3.7 years ago by WouterDeCoster 47k

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The result is:

samtools idxstats sorted_SRR1972739.bwa.bam

AF086833.2  18959   15279   11
*   0   0   5450

ADD REPLY • link 3.7 years ago by schlogl ▴ 160

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AF086833.2 =\= AF086833

ADD REPLY • link 3.7 years ago by GenoMax 141k

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You got it bro. Thank you so much! 8)

ADD REPLY • link 3.7 years ago by schlogl ▴ 160

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see my post above, the "correct" name of your reference is AF086833.2 (note the .2)

ADD REPLY • link 3.7 years ago by lieven.sterck 15k

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still not worked even with the correct name! I don't get thet error, but also get a empty file!

ADD REPLY • link 3.7 years ago by schlogl ▴ 160

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it's a fairly small region you're querying, perhaps there are just no reads mapped in that region?

try querying a bigger region (or one that you now for sure has reads mapped) to verify that your command is working (which it should as far as I can see)

ADD REPLY • link 3.7 years ago by lieven.sterck 15k

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First thing to check if the chromosome name matches in all locations. If that checks out try

samtools view sorted_SRR1972739.bwa.bam "AF086833:3050-3199" > selected.bam