User: CarnifexRex

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Posts by CarnifexRex

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Comment: C: how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... This is great. I've struggled with this for 2 days and within 30 minutes of posting here I have 3 workable ideas. Thanks to all for great and expedient suggestions. I've never worked with pysam before, but I'm always looking for new tools. Guess I'll get to reading... ...
written 6 weeks ago by CarnifexRex0
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Comment: C: how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... That seems to have successfully made the fastq files. They appear much smaller than expected, and the 2 files are of significantly unequal sizes. I was hoping to retain the original alignment information, but I'll take whatever victory I can at this point. Now I just need to do that 599 more times ...
written 6 weeks ago by CarnifexRex0
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Comment: C: how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... It's possible. At first since I couldn't see the discrepancy I thought the read listed was just last in memory, but it's consistently that read which throws the error. Since I can't get past that error I can't see if the read is listed again later on. Won't `bam2bed` remove sequence information? ...
written 6 weeks ago by CarnifexRex0
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Comment: C: how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... I did give it a try. Samtools errors out at the same point: [E::bam_read1] CIGAR and query sequence lengths differ for m01179:152:000000000-af0bb:1:1114:17516:21375 [bam2fq_mainloop] Failed to read bam record. ...
written 6 weeks ago by CarnifexRex0
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how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... Hi All, First time posting to biostars, so please forgive any formatting errors. Please let me know so I can format correctly in the future. I'm self taught at bioinf, and I've been given approximately 600 BAM files created by a old pipeline that seem to be riddled with errors. I no longer have ...
software error samtools sam/bam written 6 weeks ago by CarnifexRex0 • updated 6 weeks ago by Istvan Albert ♦♦ 82k

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