How to obtain my forward and reverse reads from sam / bam file

Question

[Bioinfo]

Hello everyone I hope you and your family and friends doing well please i need help in something my goal was to obtain unmapped reads i have my forward and reverse reads , first i mapped my data to reference genome using bowtie2 i obtained sam file and i ransfered it to bam file using samtools view and i obtained unmapped reads using

samtools view -h -f 4 input.sam > output.bam

i used samtools fastq to obtain two fastq files from bam file but when i tried assembly using shovill its shows this message:

 [shovill] Could not open pilon.changes

and i obtained 'weird results ' (great number of contigs ???)

i tried another thing to obtain my forward and reverse reads : i obtained fastq file from bam file using betools bamtofastq :

bedtools bamtofastq -i nom_de_souche_Unmapped_reads.bam -fq  nom_de_souche_Unmapped_reads.fastq

and i separated the fastq file using repair.sh :

reformat.sh in=original.fq out1=R1.fq out2=R2.fq

but it shows the same error message

Could not open pilon.changes

also in other strains it shows error message that number of forward reads is larger ... any solutions please , im stuck here

ahh i have to mention that I am connected to the remote server

Thank you very much

[GenoMax]

Hello mejait99!

Questions similar to yours can already be found at:

• how to split forward and reverse reads from sam file

We have closed your question to allow us to keep similar content in the same thread.

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

Cheers!

[Bioinfo]

hello . because the other solutions in the previous publication didn't work for me , so i tried in this question to explain more the situation and to explain the solution that didn't work for me , so it's technically not the same

[GenoMax]

It sounds like the program you are trying to use is looking for a file called pilon.changes which it can't find. Are you trying to use an assembly program meant for pacbio/nanopore reads without running/having the pilon program?

Note: I closed this question since you are asking the same thing as you did in your last question. If you can clarify that this question is independent then we will reopen it.

[Bioinfo]

i did the same thing on other reads that i download and shovill works well , anyway i will try to download pilon changes and see , thatnk you ahh i just clarified the situation , thank you

[GenoMax]

So the question as posted is not directed/relevant. It sounds like you are not following proper directions for running shovill.

Just because a program ran does not mean that it produced correct results or did the right thing. Please check the output/log files to make sure the program is doing what you think it is.