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  • olus
    replied
    Originally posted by tejaminnu View Post
    Hi Gabriel,

    I want to send u the file. which is very small. Probably u can have a look at it .. Can u just send me a mail to this id, if its not a problem.

    [email protected]

    Basically i have a Stand Alone Blast program running. The "fasta" file served as a reference file using which i blasted the large database file that i had. I am trying to find out if i can call SNP's using "Blast" program.

    And i want to confirm it by getting the SNP's using Samtools.

    Is the above explanation even valid. ?

    Do let me know


    Regards
    Teja
    Hi.
    If I understand it right, you have to:
    1) align your fasta query file (mrna_fa) to a reference with blast
    2) parse the blast output to be compliant with sam
    3) use samtools to call SNPs (to a properly indexed reference)

    for point 2) you can look at here:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    In general I can say that blast it's not suited for efficient SNP calling , but I may be wrong.

    Gabriel

    Leave a comment:


  • tejaminnu
    replied
    Hi Gabriel,

    I want to send u the file. which is very small. Probably u can have a look at it .. Can u just send me a mail to this id, if its not a problem.

    [email protected]

    Basically i have a Stand Alone Blast program running. The "fasta" file served as a reference file using which i blasted the large database file that i had. I am trying to find out if i can call SNP's using "Blast" program.

    And i want to confirm it by getting the SNP's using Samtools.

    Is the above explanation even valid. ?

    Do let me know


    Regards
    Teja

    Leave a comment:


  • tejaminnu
    replied
    Basically i have a Stand Alone Blast program running. The "fasta" file served as a reference file using which i blasted the large database file that i had. I am trying to find out if i can call SNP's using "Blast" program.

    And i want to confirm it by getting the SNP's using Samtools.

    Is the above explanation even valid. ?

    Do let me know

    Regards
    Teja

    Leave a comment:


  • tejaminnu
    replied
    Hi

    Hi Gabriel,

    I want to send u the file. which is very small. Probably u can have a look at it .. Can u just send me a mail to this id, if its not a problem.

    [email protected]

    Regards
    Teja

    Leave a comment:


  • olus
    replied
    Hi Teja.
    In theory you can convert a multifasta file in a sam (tabular) file, and then convert to bam with samtools view -b.
    But the fasta file only contains information on the nucletide sequence itself, nothing about the mapping, read quality etc... which are indeed the columns of the sam file (you will also need to rebuild the sam header).
    In conclusion I think it's useless to convert a fasta file into a sam file, but I can't exclude that you are dealing with something that requires such conversion.
    Would please briefly explain your case?

    Thank you.

    Best regards.
    Gabriel

    Leave a comment:


  • tejaminnu
    replied
    Hi Gabriel,

    Is there a way to do the opposite ? What i mean is that, i have a file called mrna_ref.fa (fasta file), can i convert it into a sam or a bam file using Samtools in the command line.

    Regards
    Teja

    Leave a comment:


  • ulz_peter
    replied
    Or picard SamToFastq:

    Works with BAM Files as well and supports some other options:

    Leave a comment:


  • olus
    replied
    This one liner would give you a fasta formatted file from a bam alignment:

    samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta

    Hope this helps.

    Gabriel

    Leave a comment:


  • Canadian_philosophy
    replied
    Thanks Maubp, I just downloaded Emboss. I will get back if I bump into trouble.
    Thanks very much.

    Leave a comment:


  • maubp
    replied
    Yes, several, including one line shell scripts.

    Possibly seqret from EMBOSS 6.3.x will do what you want.

    See also this thread for SAM/BAM to FASTQ which is very relevant:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

    Leave a comment:


  • Canadian_philosophy
    started a topic BAM/SAM to Fasta

    BAM/SAM to Fasta

    Hi there,

    I have a couple of aligned sequences from BWA. I used samtools to get the BAM format. What I really need is the Fasta format of these aligned sequences. Is there a program that would help?

    Thanks.

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