I build Indexing using this cammand:
/home/yog/software/bwa-0.7.15/bwa index Rs_1.0.cds.fasta
After that I am running BWA cammand for mapping raw reads to indexed transcripts using this cammand:
/home/yog/software/bwa-0.7.15/bwa mem Rs_1.0.cds.fasta 216.all.right.fasta 216.all.left.fasta >paired-end.aln.sam
It showing error:
/home/yog/software/bwa-0.7.15/bwa mem Rs_1.0.cds.fasta 216.all.right.fasta 216.all.left.fasta >paired-end.aln.sam [bns_restore_core] Parse error reading Rs_1.0.cds.fasta.amb
Please suggest how I can resolve it.
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The error is most likely due to the data index being formated incorrectly. In the past I have used Biopython to fix white space issues with fast files. You can use the SeqIO.convert function and "convert" it to fasta again. The function will format the fasta correctly and it should resolve the issue.
I installed biopython, if you can share the code for SeqIO will be helpful for me.
Thanks Yogesh
Sorry, time changes. If you still need it. The code should look like this.
From Bio import SeqIO
For seq in SeqIO.parsre("in.fasta", "fasta", "out.fasta", "fasta")
You can either use it in Python itself or write a quick script to accept the input from the command line.
Sorry, time changes. If you still need it. The code should look like this.
From Bio import SeqIO
For seq in SeqIO.parsre("in.fasta", "fasta", "out.fasta", "fasta")
You can either use it in Python itself or write a quick script to accept the input from the command line.
Please use ADD COMMENT to reply to earlier posts, as such this thread remains logically structured and easy to follow.
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In the command
Shouldn't you use the created index rather than the fasta file?
I did indexing first and after that I run BWA.
I build Indexing using this cammand:
/home/yog/software/bwa-0.7.15/bwa index Rs_1.0.cds.fasta
After that I am running BWA cammand for mapping raw reads to indexed transcripts using this cammand:
/home/yog/software/bwa-0.7.15/bwa mem Rs_1.0.cds.fasta 216.all.right.fasta 216.all.left.fasta >paired-end.aln.sam
Now can you suggest me how to get unmapped Right and Left reads in two separate file using samtool or sambanba cammand from the output sam file.
So, you resolved your first problem. Can you shortly comment on this?
A sam file has for each alignment a set of flags stored in one number. You can check the number you need at this web site: https://broadinstitute.github.io/picard/explain-flags.html . With samtools view -f [respectively -F] you can select those alignments having (resp. having not) this bit.