text: user9858: I Have multiple BAM files that are referenced to UCSC genome assembly GRCh37/hg19 that are read in different time frames. Now, I am planning a different studies that require assembling all the data against one assembly. Will it be possible to convert all the BAM files that I have to an upgraded version or convert the assembly to a different new assembly and how?
  I am new in this and not a bioinformatician so, if you have any questions regarding my question to answer you can ask, any type of help is highly appreciated.
  
  user9693: It is possible, with tools like CrossMap, but my recommendation is to re-align. Assemblies can change a lot between versions and your reads will undoubdedly align differently. Re-aligning is cheap, it will take a few days and you're good. Re-doing your analysis because you realize the coordinate translation messed something up will cost you much more time and energy.
  
original_text: 9858: <p>I Have multiple BAM files that are referenced to UCSC genome assembly GRCh37/hg19 that are read in different time frames. Now, I am planning a different studies that require assembling all the data against one assembly. Will it be possible to convert all the BAM files that I have to an upgraded version or convert the assembly to a different new assembly and how?
  I am new in this and not a bioinformatician so, if you have any questions regarding my question to answer you can ask, any type of help is highly appreciated.</p>
   9693: <p>It is possible, with tools like <a href="https://crossmap.readthedocs.io/en/latest/" rel="nofollow noreferrer">CrossMap</a>, but my recommendation is to re-align. Assemblies can change a lot between versions and your reads will undoubdedly align differently. Re-aligning is cheap, it will take a few days and you're good. Re-doing your analysis because you realize the coordinate translation messed something up will cost you much more time and energy.</p>
  