[maubp]

I carried out a NimbleGen array capture experimentm followed by 454 sequencing. I first used gsMapper to get a mapping assembly (output ace and fasta alignments). However, I did perform a series of subsequent manipulations : a second assembly using SSAHA2 (fasta output), some curation steps and a division of the initial alignment into segments of invariable depth of coverage (still as fasta). what would you recommend?

Thanks
Carole

Search for ACE to SAM/BAM conversion. It is possible, but you will also
need the original SFF files (or FASTQ or QUAL) for the read qualities.

[carole_smadja]

I carried out a NimbleGen array capture experimentm followed by 454 sequencing. I first used gsMapper to get a mapping assembly (output ace and fasta alignments). However, I did perform a series of subsequent manipulations : a second assembly using SSAHA2 (fasta output), some curation steps and a division of the initial alignment into segments of invariable depth of coverage (still as fasta). what would you recommend?

Thanks
Carole

[maubp]

Dear All,

I have generated a mapping assembly in fasta format and I now need to convert it into the sam format accepted by samtools.
Would anybody know a fasta2sam converter I could get access to?

Thank you very much for your assistance.

Carole

That isn't possible - FASTA files don't have enough information to describe an assembly, they can only be used to store the raw reads (without qualities or mapping information) or the contigs (without qualities or mapping information).

What assembly tool did you use? Does it have any other output files?

[carole_smadja]

fasta2sam converter

Dear All,

I have generated a mapping assembly in fasta format and I now need to convert it into the sam format accepted by samtools.
Would anybody know a fasta2sam converter I could get access to?

Thank you very much for your assistance.

Carole

[lh3]

@bioenvisage

I would encourage you to use samtools/gatk/snvmix/varscan. Soapsnp is great but others are as good and easier to use.

[rdeborja]

which script adds the header

Just wondering which script was used to add the header after the maq2sam-long conversion.

Okay, I have solved my problems. Seems there is a script to add the header file, and different command options for conversion to Bam.

[bioenvisage]

Hi Ih3,

Is there any utility/script/tool for converting SAM format to SOAP alignment output format.Iam using SOAPsnp which accepts only the SOAP aligner format.

[corthay]

Hi,

I got the following strange pileup results and I am at a loss what to do.
My data is RNA-SEQ and sam file was generated by using Tophat ( ver1.0.14 )
Is there anyone who had similar result or have any idea to solve this problem ?

Thanks
Corthay

-----------------------------------------------------------
Supercontig4 3775441 A A 36 0 60 3 .., EGD
Supercontig4 3775442 A A 36 0 60 3 .., FGC
Supercontig4 3775443 C C 36 0 60 3 .., EGB
Supercontig4 3775444 G G 36 0 60 3 .., FGD
Supercontig4 3775445 G G 36 0 60 3 .., GGD
Supercontig4 3775446 A A 36 0 19 30 ^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G^"G.., G>GCFGEGFGDGGGD>?E=3EEF#BE?AEB
Supercontig4 3775447 A A 117 0 19 30 ............................., G?GCGGEGGGDGGGBCBFB<BBG#?DBEGE
Supercontig4 3775448 G G 36 0 19 30 TTTTTTTTTTTTTTTTTTTTTTTTTTT.., F>G5EDBBEGDFGGBA?D@-B?D#??AEGE
Supercontig4 3775449 A A 36 0 19 30 CCCCCCCCCCCCCCCCCCCCCCCCCCC.., G:GBFGCGGGCGGFECCA:?B5D?BDCEGE
Supercontig4 3775450 A A 36 0 19 30 GGGGGGGGGGGGGGGGGGGGGGGGGGG.., G<G?GGEGGG?GGGDCEB::BAFA@ECBDD
Supercontig4 3775451 T T 36 0 19 30 AAAAAAAAAAAAAAAAAAAAAAAAAAA.., GBGDGGEGGG?GGGEBCDB?:?GA?G?BGA
-----------------------------------------------------------

[aby]

Okay, I have solved my problems. Seems there is a script to add the header file, and different command options for conversion to Bam.

[lh3]

http://samtools.sourceforge.net/mpileup.shtml

[seq_GA]

Hi Heng,

Can you please explain about the new feature of samtools (ie) multisample pile up? Thanks.

[swbarnes2]

samtools import example.sam example.bam

This command does not work. Gives error:

Usage: bamtk import <in.ref_list> <in.sam> <out.bam>


What to do? What is in.ref_list ?

Use faidx to make a .fai file, use that for the in.ref.list. It works for me.

[AXW]

Does anybody know of a utility/script for converting .SAM/BAM files into .SOAP? I know that there are scripts out there to go from SOAP->SAM, but I can't find anything going the other way.

Cheers.

[aby]

sam to bam conversion not taking place

samtools import example.sam example.bam

This command does not work. Gives error:

Usage: bamtk import <in.ref_list> <in.sam> <out.bam>


What to do? What is in.ref_list ?

[NF_seq]

Question about the output of bwa?

I got the output, see below:
HWI-EAS307:1:54:758:902#0 20 19641_CLSZ1904.b1_P20.ab1_CLSZ_L._sativa_library_forward_335 301 20 36M * 0 0 CAAATCGGTGTGTTTTCACTGGTCGTGCTCGTTCCG aabaaaaaaaaababaa`aaaabaabaabbabaaaa XT:A:U NM:i:1 X0:i:1 X1:i:2 XM:i:1 XO:i:0 XG:i:0 MD:Z:35T0 XA:Z:13134_QGB27J17.yg.ab1_QGB_L._sativa_library_forward_448,-58,36M,2;7061_CLS_S3_Contig6993_CLS_S3_L._sativa_library_forward_968,-404,36M,2;

I can not understand the flag value 20. I used "samse" to process single reads.
"XT:A:U" indicates the read uniquely mapped to the reference, why i still got XA for alternative alignment inforamtion?
It is confused me. Someone could help me a bit for that? Thank you very much

It's also confused me that "XT:A:U" and "XA:..." information came up in one alignment. Could anyone please explain that? Thanks a lot! And if i only care about uniquely mapped reads, is this kind of reads what i want?