Timeline for Alignment QC differences between HISAT2 and Qualimap
Current License: CC BY-SA 3.0
7 events
| when toggle format | what | by | license | comment | |
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| Feb 16, 2018 at 8:30 | comment | added | beginner | Reads alignment reads aligned (left/right) = 86,704,161 / 85,485,519 read pairs aligned = 83,397,732 total alignments = 244,302,519 secondary alignments = 72,112,839 non-unique alignments = 22,973,098 aligned to genes = 249 ambiguous alignments = 25 no feature assigned = 9,759 not aligned = 5,887,822; Reads genomic origin exonic = 249 (2.49%) intronic = 693 (6.92%) intergenic = 9,066 (90.59%) overlapping exon = 54 (0.54%) Transcript coverage profile 5' bias = 0.39 3' bias = 10.04 5'-3' bias = � | |
| Feb 16, 2018 at 8:29 | comment | added | beginner | Thanks for the answers. I have to tell you that for "alignment" with HISAT2 I didn't use any gtf file. I used only standard genome index from HISAT2 website. I used gencode new version (gencode.v27 with both protein and non-coding genes) gtf for Stringtie tool. In the above qualimap result I didn't mention the paired-end option "-pe". So, I have rerun the qualimap again with "-pe" and also "-p strand-specific-reverse" which is RF in HISAT2. The following are the results. | |
| Feb 15, 2018 at 23:20 | comment | added | Devon Ryan | @raju I've updated my reply. | |
| Feb 15, 2018 at 23:19 | history | edited | Devon Ryan | CC BY-SA 3.0 |
added 1045 characters in body
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| Feb 15, 2018 at 21:59 | comment | added | beginner | And what are the causes reads genomic origin - Intergenic shows higher number? sequencing error, mapping error, unannotated genes? I see in some of the post that for human genome, it's very likely cz of unannotated gens. The annotation of a genome could never be finished, as it could never be sequenced completely. Is this right? | |
| Feb 15, 2018 at 21:01 | comment | added | beginner | thankyu !! what are those nUmber of secondary and non-unique alignments, ambiguous, and no feature aligned? | |
| Feb 15, 2018 at 20:34 | history | answered | Devon Ryan | CC BY-SA 3.0 |