Question: is our reads needs indexing before alignment like refrence genome or not ? some one explain to me plz
0
gravatar for sabaghianamir70
18 months ago by
iran
sabaghianamir7010 wrote:

im new in this matter. and read some papers and watch some tutorial videos. i am in the way of aligning my dara. but in igv my data dosent match with my reference genome even iv got 92.7 % overal alignment with hisat2. some one help me pz

rna-seq alignment • 462 views
ADD COMMENTlink modified 18 months ago by h.mon30k • written 18 months ago by sabaghianamir7010

but in igv my data dosent match with my reference genome

what is "my data" ?

ADD REPLYlink written 18 months ago by Pierre Lindenbaum129k

Saccharomyces cerevisiae. i think its some thing wrong with my samtools

ADD REPLYlink written 18 months ago by sabaghianamir7010

Probably you are loading wrong genome in IGV. Check reference version in IGV and it should match the reference you have used in alignment sabaghianamir70

ADD REPLYlink written 18 months ago by cpad011213k

no i dont think so,. in igv i chose Saccharomyces cerevisiae refrence genome. both versions are same.

ADD REPLYlink written 18 months ago by sabaghianamir7010
1
gravatar for h.mon
18 months ago by
h.mon30k
Brazil
h.mon30k wrote:

Both reference genome in fasta format and mapped reads file in bam format need to be indexed, and the bam file needs to be sorted as well. For the fasta reference:

samtools faidx ref.fasta

For the mapped bam:

 samtools sort -o sorted.bam mapped.bam
 samtools index sorted.bam

In addition, the reference genome loaded into OGV need to be the same used for mapping.

ADD COMMENTlink written 18 months ago by h.mon30k

i think that is my problem , samtools wont work .im trying to install it for 2 days. its really annoying. i have the same problem as he had error installing samtools on ubuntu . but eventually is see this

libncurses5-dev : Depends: libtinfo5 (= 6.1-1ubuntu1) but 6.1-1ubuntu1.18.04 is to be installed Depends: libncurses5 (= 6.1-1ubuntu1) but 6.1-1ubuntu1.18.04 is to be installed Depends: libtinfo-dev (= 6.1-1ubuntu1) but it is not going to be installed

and the libtinfo-dev does not work.

ADD REPLYlink written 18 months ago by sabaghianamir7010
1

If you are not able to install samtools, you can use igvtools (http://software.broadinstitute.org/software/igv/igvtools) for sorting and indexing. IGV ui has igvtools as menu option. If you have dependency issues in installation, try conda (user space installation). sabaghianamir70.

ADD REPLYlink modified 18 months ago • written 18 months ago by cpad011213k
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