[wuhoucdc]

Hi lh3,

Does SAMtools call SV currently? Thanks

Wuhoucdc

[luisczul]

Maq2Sam not working propertly?

Hello,

I ran the script Maq2Sam on my mapping files and the pileup file coming from the sam file is not even as close (in size and number of bases assembled) as the maq pileup file.

Does anybody know how to fix this? Or maybe another way to go from Map. files from maq to samtools?

Thanks,

[NSTbioinformatics]

Just modified a few lines of export2sam.pl to the new script sorted2sam.pl
sorted2sam.pl works very well to process S_N_sorted.txt (eland alignment) for single reads.
I did not test to it to parse paired end reads. It may not work well.

If someone wants to the script, please send email to [email protected]

Thank everyone for giving me some help.

By the way, i am going to the Illumina user symposim in April 27-29 in spain. I may meet someone of you there.

[kjngo]

Thank you lh3

[NSTbioinformatics]

Thank you Li Heng and Kmcarr.
I did not pay attention to the slight difference of s_N_export.txt and s_N_sorted.txt.

I will try to modify export2sam to sorted2same, hope i could find time to do so.

We are happy to the result of eland (illumina pipeline 1.5) that mapped 72.46% of unique mapped reads, while maq mapped 62.71% of unique mapped reads with the same setting of allowing at most 2 mismatches.

[lh3]

@kjngo

This is a known bug in bwa (not samtools). Please check out the latest SVN with:

svn co https://bio-bwa.svn.sourceforge.net/...-bwa/trunk/bwa bwa

[kjngo]

can someone please help me with this error in BWA/Samtools:

[samopen] SAM header is present: 89 sequences.
[sam_read1] reference '29118' is recognized as '*'.
Parse error at line 3165090: sequence and quality are inconsistent
/opt/gridengine/default/spool/compute-0-6/job_scripts/204180: line 20: 20739 Aborted (core dumped) /share/apps/samtools/samtools view -bS Tso7_Lib1_CTAG_aln.sam >Tso7_Lib1_CTAG_aln.bam
[bam_sort_core] truncated file. Continue anyway.

sorry I am new at this.

[lh3]

export2sam.pl was developed when CASAVA was not formally released (GApipeline<1.0). I do not have access to export files any more and I cannot fix the problem. Is anyone interested in maintaining this script? Thanks in advance.

In addition, I would also recommend to remap your reads with bwa/novoalign if you have the capacity. I am not familiar with the latest version of eland. But the old version was not as accurate as the best 3rd-party aligners.

[kmcarr]

Yes, you are right.
.../samtools-0.1.7a/misc/export2sam.pl
does not work for s_N_sorted.txt and s_N_export.txt from GA pipeline 1.5

Any other solution?

NST,

Did you try the script on the s_N_export.txt file or the s_N_sorted.txt file? The script will work on an export file (as the name implies) but not on a sorted file. The last column of the export file shows whether the read in question is a PF read or not [Y/N]. Since the sorted file only includes PF reads this column would be redundant so it is omitted.

export2sam.pl checks the value of this column. If you provide s_N_sorted.txt as an input file the column will be absent and export2sam.pl will through a stream of errors along the lines of:

Use of uninitialized value in string ne at /usr/local/samtools/export2sam.pl line 67, <$fh1> line xxxxxx.

Here is workaround of you must use the s_N_sorted.txt. Add "<tab>Y" to the end of every line of your sorted file.

[NSTbioinformatics]

Do you have more experience about converting eland to sam or maq to share with us?

Although writing a script to convert eland format and sam format is not difficult, it will cost some time.

[ikrier]

I found that there are few programs that actually handle 1.3+ formats. I resort to realigning everything, even though the output of my in-house Chipseq facility is eland format. Most people around here do it like that, anyways, and either use Bowtie, Maq or bwa.

[NSTbioinformatics]

Li Heng, could you help us solve it?

Thank you very much.

[NSTbioinformatics]

Yes, you are right.
.../samtools-0.1.7a/misc/export2sam.pl
does not work for s_N_sorted.txt and s_N_export.txt from GA pipeline 1.5

Any other solution?

[ikrier]

To lparsons:

After you compile samtools with "make", you will find "maq2sam-short" and "maq2sam-long" in the "misc/" directory. There is also a script "export2sam.pl" that converts Illumina's export to SAM. I have not thoroughly tested this script on all export files, though.

So this doesn't work for Illumina 1.3+?

[NSTbioinformatics]

Thank you very much. Indeed after installing curses-lib pakage. It works

However......
I still don not know to use SAMtool to convert eland alignment into sam format

Does someone have experience about it?