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Forum: Bioinformatics 10-17-2011, 01:43 PM
Replies: 1
Views: 2,074
Posted By totalnew
samtools tview

Hi, all

I've used samtools tview for few days, I do see the reads in upper and lower cases, and I assumed that they are in opposite strand, but all of sudden I want to confirm this, seems I...
Forum: Bioinformatics 05-06-2011, 11:21 AM
Replies: 0
Views: 4,338
Posted By totalnew
mutiple mapped reads FLAG/TAG in bwa alignment data

Hi, All


I am doing analysis on bwa alignment data. I have a question about multiple mapped reads, what I like to do is to identify/filter any pairs that one or two reads of the pair is/are...
Forum: Bioinformatics 01-08-2010, 10:52 AM
Replies: 48
Views: 53,604
Posted By totalnew
Currently in most of sam/bam files, the header is...

Currently in most of sam/bam files, the header is empty. However, this could potentially be a good place to store all the info people are interested. From the SAM format specification, HEADER SECTION...
Forum: Bioinformatics 01-06-2010, 04:36 PM
Replies: 48
Views: 53,604
Posted By totalnew
Flag 0 means "the read is not paired and mapped,...

Flag 0 means "the read is not paired and mapped, forward strand"

You are right, MAPQ =0 is an indication that this read has multiple best hits, which means it is not unique match.
Forum: Bioinformatics 12-11-2009, 11:39 AM
Replies: 3
Views: 2,863
Posted By totalnew
the number of aligned reads by maq and bwa

We have applied maq and bwa to align the same production data, and we see an obvious difference on the number of aligned reads between maq and bwa, especially a decrease in the number with longer...
Forum: Bioinformatics 10-30-2009, 02:10 PM
Replies: 6
Views: 15,142
Posted By totalnew
That is clear enough, thanks a lot!

That is clear enough, thanks a lot!
Forum: Bioinformatics 10-30-2009, 09:58 AM
Replies: 6
Views: 15,142
Posted By totalnew
Sorry, I still don't understand.

Sorry, I still don't understand.
Forum: Bioinformatics 10-29-2009, 11:04 AM
Replies: 6
Views: 15,142
Posted By totalnew
bwa mapping quality

bwa approximate mapping quality in such way,

{.
.
.
if (p->c1 == 0) return 23;
if (p->c1 > 1) return 0;
if (p->n_mm == mm) return 25;
if (p->c2 == 0) return 37;
n = (p->c2 >= 255)?...
Forum: Bioinformatics 10-20-2009, 10:07 AM
Replies: 18
Views: 14,827
Posted By totalnew
You should sort bam file, try this samtools...

You should sort bam file, try this

samtools sort -n aln.bam sorted

then mv the sorted.bam file to whatever name you want.
Forum: Bioinformatics 08-27-2009, 04:14 PM
Replies: 5
Views: 3,370
Posted By totalnew
I am still running the program, the tool is very...

I am still running the program, the tool is very easy to use, but I may have questions during the running, I will track this thread to post all problems I meet.
Forum: Bioinformatics 08-25-2009, 01:16 PM
Replies: 5
Views: 3,370
Posted By totalnew
BreakDancer problems

Does anyone ever use BreakDancer to detect GSV?

I downloaded it from http://genome.wustl.edu/tools/cancer-genomics, but I found I can't run it successfully, I don't know if I use correct command,...
Forum: Bioinformatics 08-21-2009, 03:09 PM
Replies: 19
Views: 20,876
Posted By totalnew
I had this problem too, my solution was to use...

I had this problem too, my solution was to use unix command to trim and fold the fasta file. You would have to cut the header first, and catenate it with your sorted fasta file. It perfectly solves...
Forum: Bioinformatics 08-14-2009, 09:38 AM
Replies: 48
Views: 53,604
Posted By totalnew
You are right, sam file is quite large size, from...

You are right, sam file is quite large size, from my simulation, the sam file is generally four times larger than corresponding bam file. My idea is to write a script to generate sam file and further...
Forum: Bioinformatics 08-13-2009, 12:37 PM
Replies: 48
Views: 53,604
Posted By totalnew
Output of maq is map file, use maq mapview to...

Output of maq is map file, use maq mapview to make it visible and count the lines which can be done by unix command. The output of bwa is sam file which is human readable, you should be able to open...
Forum: Bioinformatics 08-13-2009, 11:47 AM
Replies: 4
Views: 1,957
Posted By totalnew
It still mixed me up, I thought NM (edit...

It still mixed me up, I thought NM (edit distance) is more or less similar to "number of mismatches of the best hit" defined in MAQ manual. I ever parsed the maq output (.map) file, the distribution...
Forum: Bioinformatics 08-13-2009, 10:36 AM
Replies: 4
Views: 1,957
Posted By totalnew
Tags NM, H0 and H1 are quite confusing, I discuss...

Tags NM, H0 and H1 are quite confusing, I discuss it in this thread, please take a look,
http://seqanswers.com/forums/showthread.php?t=2258

The read you listed above could be interpreted in two...
Forum: Bioinformatics 08-13-2009, 09:54 AM
Replies: 48
Views: 53,604
Posted By totalnew
The flag number is decimal value, I wrote a small...

The flag number is decimal value, I wrote a small tool to convert decimal to Hex and binary string, but it was rarely used. Firstly, you can easily identify if this read is paired (even: SE ; odd:...
Forum: Bioinformatics 08-12-2009, 09:54 AM
Replies: 48
Views: 53,604
Posted By totalnew
FLAG field is normally associated with other...

FLAG field is normally associated with other attributes to parse the read, likely, if this read is mapped, if this red is paired..... see the description table in samtools manual.

For MAPQ...
Forum: Bioinformatics 08-10-2009, 09:18 AM
Replies: 18
Views: 14,827
Posted By totalnew
Apparently, you shouldn't use samtools view sam...

Apparently, you shouldn't use samtools view sam file, that is for bam file. To pileup, you would either make bam file or get indexed reference sequence (.fai).
Forum: Bioinformatics 08-10-2009, 09:06 AM
Replies: 18
Views: 14,827
Posted By totalnew
That is way simple, try this linux command ...

That is way simple, try this linux command

samtools view test.bam > test.sam
Forum: Bioinformatics 08-09-2009, 04:12 PM
Replies: 8
Views: 6,183
Posted By totalnew
Yes, for 75bp read, you may have to use...

Yes, for 75bp read, you may have to use maq2sam-long, otherwise, otherwise you will get seg fault :<.

I have not downloaded new samtools, I guess it will be more handy to use samtools view -x. For...
Forum: Bioinformatics 08-07-2009, 09:18 AM
Replies: 8
Views: 6,183
Posted By totalnew
1. There is an excutable file "maq2sam" come with...

1. There is an excutable file "maq2sam" come with samtools package to allow you convert maq out to sam format.

2. For FLAG field, if you want to parse it, simply use $FLAG & 0x01(02, 20, 20..) to...
Forum: Bioinformatics 08-06-2009, 02:15 PM
Replies: 0
Views: 1,700
Posted By totalnew
hits information in sam file

I am unclear about the hit number (H0, H1) and edit distance (NM) in sam file, the detailed discussion is in thread:
http://seqanswers.com/forums/showthread.php?t=2258

Welcome to post comments...
Forum: Bioinformatics 08-06-2009, 01:59 PM
Replies: 15
Views: 4,916
Posted By totalnew
I don't get your point. If you want to view...

I don't get your point.

If you want to view maq output, use maq mapview .....
Forum: Bioinformatics 08-06-2009, 01:06 PM
Replies: 15
Views: 4,916
Posted By totalnew
Yes, you should be able to know, since they are...

Yes, you should be able to know, since they are actually same. NM in sam is obtained from field "number of mismatches of the best hit", H0 is from field "number of 0-mismatch hits of the first 24bp",...
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