Confused about the number of reads #1924
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sodiumnitrate
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Hi Irem, Mapping long reads (>300b) requires STARlong executable. |
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Thank you for the info. I compiled and used Here's the command: The stdout is as follows: |
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Hi, I'm trying to map sequences from a
.fastafile. The file contains about 2,800,000 sequences. However, the output alignment file has 259 reads. Is STAR somehow merging similar sequences? TheLog.final.outfile says only 30 are unmapped (see below).Further, the sequences in the
.fastafile have names in the following formatname/XXXX/ccswhereXXXXis a number. However, the outputSAMfile has all the read names listed asname. I tried adding-readNameSeparator "_"but that didn't solve the problem.Here's the command I ran:
What could I be missing? There were no error messages in the Log files or otherwise. This is
Log.final.out:Beta Was this translation helpful? Give feedback.
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