161222 Back to work - npslindstrom/DE-analysis GitHub Wiki

I have been suffering from a cold the last few days and had some Christmas time family things so work has been slow but today I getting back to work.

I have been trying to do alignments with star but it seems like it is still not working properly. I have been feeding in two duplicates of the same sample but only one alignment file is generated. In the logs it says that 98% of the reads are unmapped due to being to short. I am currently troubleshooting what that might mean.

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Since Linnea has been having the same problem with her alignment I tried to run FastQC on the raw reads and it seems like the reads are actually around 50bp in length. In hindsight this should of course have been the first step of the analysis...

Anyway, since we generated the genome index supposing that the reads would be closer to 100 this might explain why so many reads are unmapped due to being short. I will try to redo the genome indexing using a sjdboverhang option of 50 rather than 100 and then redo the mapping using this reference.

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I remade the genome index as detailed above but it made no difference to the mapping. I will continue troubleshooting.