BAM file manipulations

Question: BAM file manipulations

3.5 years ago by

United Kingdom

d.angra • 50 wrote:

I have made a whole assembly of RNA seq data using Trinity. The assembled file generated has been aligned with my choice of dataset to identify SNPs. The first step was alignment which I have manged to do by using BWE. But I am experiencing some problems in this output which is in the form of BAM file. I tried to Add or replace read groups using 'NGS Piccard' . When I try to visualise it in IGV it said

"Cannot add sequence that already exists in SAM Sequence Dictionary"

In order to resolve this I want to clear and edit the headers. I am not able to find which will be a suitable tool to for this.

Any suggestions what can I do?

Can anybody please tell me what this means and why is this error coming from?

Thanks

Deepti

samtools • 1.1k views

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modified 3.5 years ago • written 3.5 years ago by d.angra • 50

3.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Deepti,

If you want to custom modify a SAM header, then doing this with a text editor could be the quickest route. You can use Galaxy to split the SAM dataset into two using "Select" (one with just the header, the other with just the data lines), download the header dataset, modify, upload, then merge using back with the data lines using "Concatenate".

Stick with a plain text editor and avoid MS Word (or others) since they can add in hidden characters that will cause problems downstream.

Now, that said, tools in Galaxy can perform many file manipulations, so that is just one option. The groups "Text Manipulation" and "Filter and Sort" contain the most used options. I only recommended the manual edit in this case because I know that you are familiar with these tools already and am guessing that they are not able to perform the exact operation you wish to do.

Good luck! Jen, Galaxy team

ADD COMMENT • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

3.5 years ago by

d.angra • 50

United Kingdom

d.angra • 50 wrote:

Hi Jen,

Thankyou very much. I am trying this now.

Deepti

ADD COMMENT • link written 3.5 years ago by d.angra • 50

3.5 years ago by

d.angra • 50

United Kingdom

d.angra • 50 wrote:

Hi Jen

I am unable to figure out the exact tool to be used. With SAM tools I could not find an option of selecting the header etc.I want to confirm with you that is this the only way to resolve the error which I mentioned above.

Another small query is my galaxy server is working too slow. Is it because of my datasets or any other issue. Please could you help me with this too.It is taking very long to load the history items, sometimes it doesnt happen also. Any body else facing the same problem?

Viva

ADD COMMENT • link written 3.5 years ago by d.angra • 50

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