Mapping with segemehl

Question

[neha 114]

Hello everyone

I am working on segemehl and this tool is new to me. I have used the list of following commands in given order, but obtaining no results for my test data (empty .bed files).

I will be highly thankful if anyone could suggest me the problem.

Here are the commands:

./segemehl.x -d ce6_eg.fa -x ce6.idx
./segemehl.x -i ce6.idx -d ce6_eg.fa -q SRR2104398_1.fastq -p SRR2104398_2.fastq > map_reads.sam

(for sorting)

samtools faidx ce6_eg.fa
samtools import ce6_eg.fa.fai map_reads.sam map_reads.bam
samtools sort map_reads.bam map_reads.sorted
samtools view -h map_reads.sorted.bam > sorted_map.sam
./testrealign.x -d ce6_eg.fa -q sorted_map.sam -n

Kindly suggest please

[Michael]

what's in map_reads.sam? Maybe it's not even a problem with segemehl. Also, I don't see where the bed files should come from.

[neha 114]

Really thanks for your reply.

The result of mapping of reads with the reference transcriptome is stored in .sam file. And after running the test realign.x command these bed files are generated.