Re: Account to upload

[Tin Chi Nguyen]

I run the SAM file you gave me and I noticed that this is an alignment against cDNA. Currently SAMMate only processes the alignment result against the reference genome.
Can you upload the alignment file (SAM/BAM) against the reference genome please?

Thanks

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From: "behrooz darbani" <behrooz...@gmail.com>
To: "Tin Chi Nguyen" <ex6...@wayne.edu>
Sent: Saturday, February 9, 2013 5:10:13 PM
Subject: Re: Account to upload

This one is against cDNAs.

However, I had also tried the genome.

 

Regards,

Behrooz

On Sat, Feb 9, 2013 at 4:36 PM, Tin Chi Nguyen <ex6...@wayne.edu> wrote:

Hi Behrooz,

I have another question: did you align the reads against the reference genome (or DNA contigs)?

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[Tin Chi Nguyen]

Hi Behrooz,

I will look into it soon. Thanks

Btw, what aligner did you use this time?

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From: "behrooz darbani" <behrooz...@gmail.com>
To: "Tin Chi Nguyen" <ex6...@wayne.edu>

Sent: Monday, February 11, 2013 7:48:07 AM

Subject: Re: Account to upload

Hi Tin 

Now you find the SAM file (using genome sequence) and the annotation files both in the folder you have made named behrooz.

Regards,

Behrooz

[Tin Chi Nguyen]

Hi Behrooz,

I think bowtie2 is able to align reads with gaps. However it cannot replace junction aligners and will miss a lot of splicing events

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From: "behrooz darbani" <behrooz...@gmail.com>
To: "Tin Chi Nguyen" <ex6...@wayne.edu>

Sent: Tuesday, February 12, 2013 3:20:51 AM

Subject: Re: Account to upload

Hi Tin, You are right I checked it using chromosome 1 and that works.

It seems the whole genome seq is somehow not correct.

Thanks for your efforts. 

I have a ?. the last time when I aligned the reads against chr. 1 and analyzed it by sammate, it reported both exon and exon-exon junction reads. However I had used the bowtie in alignment.  Is it possible? Is bowtie able to do this?

On Tue, Feb 12, 2013 at 12:27 AM, Tin Chi Nguyen <ex6...@wayne.edu> wrote:

Hi,

I check the file Hordeum_vulgare.sam, the alignment is still against the cDNA sequences.
If you check the gtf file, you will see the following lines:

morex_contig_2669042    protein_coding  exon    2       251     .       -       .        gene_id "MLOC_42952"; transcript_id "MLOC_42952.1"; exon_number "1"; seqedit "false";
morex_contig_2669042    protein_coding  CDS     16      249     .       -       0        gene_id "MLOC_42952"; transcript_id "MLOC_42952.1"; exon_number "1"; protein_id "MLOC_42952.1";
morex_contig_2668822    protein_coding  exon    118     275     .       +       .        gene_id "MLOC_42947"; transcript_id "MLOC_42947.1"; exon_number "1"; seqedit "false";
morex_contig_2668822    protein_coding  CDS     118     273     .       +       0        gene_id "MLOC_42947"; transcript_id "MLOC_42947.1"; exon_number "1"; protein_id "MLOC_42947.1";
morex_contig_2668583    protein_coding  exon    3       231     .       +       .        gene_id "MLOC_42936"; transcript_id "MLOC_42936.1"; exon_number "1"; seqedit "false";


In which morex_contig_2669042 is a DNA sequence, MLOC_42952.1 is a cDNA sequence. However, the SAM header looks as follows:
@HD     VN:1.0  SO:unsorted
@SQ     SN:MLOC_7.2     LN:255
@SQ     SN:MLOC_16.1    LN:474
@SQ     SN:MLOC_30.1    LN:444
@SQ     SN:MLOC_31.1    LN:198
@SQ     SN:MLOC_44.1    LN:402


which means that you aligned against the cDNAs, not the DNA sequences.