Tracking The Reads In A Deno Assembly

Question

[rehma.ar]

hi all!

i have a very simple question which may not be very simple,

i have extracted some reads from a bam file, and have made a denovo assembly using soapdenovo. then i blast these contigs against my reference genome. i got some hits. but the reads belong to different positions in the bam file. so i know the position of the hit in the reference genome but i also want to know the position in the bam file. but soapdenovo does not keep track of the reads in the assembly.

if i could get the information that during assembly, which read went to which contig that would solve my problem.

i was wondering if there is another assembler that keep tracks of the reads in the assembly would be great or any other indirect solution.

Answer 1

[lelle]

Velvet can be configured to do read tracking.

Look in the manual section 3.2.4

Answer 2

[rehma.ar]

thanks alot for the response but i am facing a problem here i have used velvet to make the assembly using this command

./velveth outputdirectory 25 -bam -shortPaired .bam

and then

./velvetg outputdirectory/ -mincontiglgth 100 -inslengthlong 300 -readtrkg yes -amosfile yes

and i got the the result. the read traking should be in the file "LastGraph" a very small portion of the file looks like this.

NR 29 113

1294 52 0

1299 49 0

which should be innterpretted as

NR $NODEID $NUMBEROFSHORTREADS $

READID $OFFSETFROMSTARTOFNODE $STARTCOORD

$READ_ID2 etc

. but "1294" and "1299" are not exactly the read ids and i don't have them in my .bam file. what do you think is going wrong in here.

[lelle]

It has been a while since I worked with this, but I think these are the read IDs velvet is using internally.

In the output folder there should be a file called "Sequences". It is basically a fasta file with the input reads. The fasta header should look like this:

> M00298:13:000000000-A1BJE:1:1101:17340:1510 2:N:0:1    6       1

It starts with the original read ID followed by the vlevets internals read ID (6 in this case). I do not know at the moment what the last number means.

[rehma.ar]

it was really helpful. actually there was no description of the "Sequences" file in the manual.

thanks alot