Question: (Closed) Python script that converts sorted and indexed BAM (BAI) file into TSV(Tab Separated) file
0
gravatar for malikbashirkhan2
4.2 years ago by
Pakistan
malikbashirkhan20 wrote:

Dear all...

We have a file with "BAI" format and need to convert it to "TSV" format using python script.

We need a python script that converts .BAI file into "TSV".

I am a beginner at python scripting.

pysam python htseq • 2.0k views
ADD COMMENTlink modified 4.2 years ago by RamRS25k • written 4.2 years ago by malikbashirkhan20
2

Please try something yourself before asking the comunity to provide you with ready-made scripts. Please don't use all caps. Did you check samtools?

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Dr. Mabuse47k

Hello malikbashirkhan2!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4.2 years ago by Dr. Mabuse47k

hello Michael Dondrup!

the question u have found at thread How Can I Convert Bam To Sam? is different from our question because we are converting the file from bai to tsv. not from bam to sam .

ADD REPLYlink written 4.2 years ago by malikbashirkhan20

SAM is a tab separated format, unless you are more specific, there is nothing to do for us. A bai file is just the index of a bam file. Which useful information do you want to extract from a bam index?

ADD REPLYlink written 4.2 years ago by Dr. Mabuse47k

i want to convert it into tsv (tab seperated value) which i can easily convert it into spread sheet format.

ADD REPLYlink written 4.2 years ago by malikbashirkhan20

SAM is tab separated. SAM data on spreadsheets is a REALLY BAD idea.

ADD REPLYlink written 4.2 years ago by RamRS25k

Try to open a SAM file in Excel, then you will see why do not want to convert into spread sheet format.

ADD REPLYlink written 4.2 years ago by Dr. Mabuse47k

Emphasizing what Michael said, please don't use all caps, because it is rude.

ADD REPLYlink written 4.2 years ago by RamRS25k
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