[kenietz]

Hi Lizex,
im sorry for the late reply, im very busy lately and could not find time. But better later than never

firstly it seems to me you compiled samtools before, i mean when you first installed the program. Then, try this:
1 Edit the source file
2 make clean
3 ./configure
4 make


This should work.

'Permission denied' shows that the program is owned most probably by root and you try running it as user. Two things possible here:
1. Copy/Move the program to a place in your PATH.
2. Change the owner of the file to be your user with 'chown'. Check 'man chown' for syntax. Also you need to be root to use chown.

Else provide me with email n i will send you the compiled version of modified samtools plus last version of my script.

Cheers

[Lizex]

Hi Kenietz
Thanks for the reply.
I've send the my e-mail adress.

Regards

[YazBraimah]

Kenietz,

I just used your script and it works beautifully. Thanks for writing it.

Yaz

[kenietz]

Hi YazBraimah,
glad to hear that it worked for you

Cheers

[YazBraimah]

FYI,

A Trinity plug-in can also do this. See:

http://transdecoder.sourceforge.net/

under "Starting from a genome-based transcript structure GTF file (eg. cufflinks)"

YB

[xmubingo]

Here is the process that I am using:

samtools mpileup -uf ref.fa accepted_hits.bam | bcftools view -cg - | vcfutils.pl vcf2fq | fq2fa.pl > new_ref.fa
gffread -w transcripts.fa -g new_ref.fa transcripts.gtf

where fq2fa.pl is a bioperl script to convert from fq to fasta

I also have an email into the cufflinks developers to see if there is a way that the gffread utility can be enhanced to get the consensus sequence from the bam file and not the reference genome.

Hi pkerrwall, I used commands same as yours. but i found that sequences in cns.fq generated by fq2fa.pl have different length with them in reference sequences. do you know why?

[yueluo]

Hi pkerrwall, I used commands same as yours. but i found that sequences in cns.fq generated by fq2fa.pl have different length with them in reference sequences. do you know why?

Take a look at this post:

http://seqanswers.com/forums/showthread.php?t=35066

As gringer mentioned:

But bear in mind that the vcf2fq script is designed for SNPs, not INDELs. If there is an INDEL in your sequence relative to the reference, then the INDEL and a few flanking bases will be changed to lower case, but not replaced. This means that any fastq file generated from this script will have the same length as the input reference sequence.

I sent a patch to their sourceforge page to fix this (and allow more compact partial vcf files with a provided reference sequence), but I don't think it's been implemented yet.

[xmubingo]

Take a look at this post:

http://seqanswers.com/forums/showthread.php?t=35066

As gringer mentioned:

Thanks, yueluo!! I asked gringer, and he replied. I guess some incorrect operations in my pipeline.

[kiran0991]

Hi All,

I use Bowtie/TopHat/cufflink to analyze the RNA-Seq. I want to extract the rebuild transcripts by these softwares. However, I can only the BED file. Can anyone give idea to extract these assembled transcript sequence?

Thanks,
ZC

To extract the assembled transfrags from cufflink, following command is useful

$gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

Source : Cufflink