GulayBenguUlukaya
commented
1 year ago Hello! Thank you for this tool to analyze CRISPR screen data. We're as a lab just starting to analyze some CRISPR drug screen projects, and in the two times we tried using this tool, we ran into the same trouble. We're having the issue that when I want the software to automatically determine trim-5 length, I get the error below. When I instead set "--trim-5 23", I get max 10% alignment in all samples. Can you think of any solution for this? Thank you so much!!
Best, Gulay B. Ulukaya BiNGS Core at Mount Sinai
Error message: INFO @ Tue, 01 Aug 2023 09:53:34: Auto determination of trim5 results: 30,29,28,23,26,25 INFO @ Tue, 01 Aug 2023 09:53:34: Determining the trim-5 length of FASTQ file EG03_01_R2_001.fastq.gz... INFO @ Tue, 01 Aug 2023 09:53:34: Possible gRNA lengths:20 INFO @ Tue, 01 Aug 2023 09:53:34: Processing 0M reads ... INFO @ Tue, 01 Aug 2023 09:53:38: Read length:75 INFO @ Tue, 01 Aug 2023 09:53:38: Total tested reads: 100001, mapped: 0(0.0) ERROR @ Tue, 01 Aug 2023 09:53:38: Cannot automatically determine the --trim-5 length. Only 0.0 % of the reads can be identified.
The first 20 lines of one sample, in case relevant: @NB502110:449:HHJH7BGXT:1:11101:24029:1050 1:N:0:TTGAACCG CAACTNTGGAAAGGACGAAACACCGAGCCNNGNATCTCCTTCTGAGTTTTAGAGCTAGAAATAGCAAGTTAAAAT + AAAAA#EA6EEEEEEEE//EE6AEA/E/E##A#EE<<AEE///EA/E/EE</E/<AAA/AEE/<<EEEA/EE/EE @NB502110:449:HHJH7BGXT:1:11101:26316:1053 1:N:0:TTGAACCG ACGCAACTTGTGGAAAGGACGAAACACCGGNCNGCGGCAAAGCGCACTGGTTTTAGAGCTAGAAATAGCAAGTTA + /AAAAEE6EEEEEEEEEEEEEEEEEEEE/E#E#EAEEEEEAEAAEEEEAAEEEEEEEEEEEEEEEEEEEEEAEEA @NB502110:449:HHJH7BGXT:1:11101:16860:1053 1:N:0:TTGGACCG ACGCAACTTGTGGAAAGGACGAAACACCGGNGNGGTCTTTCGACCACTCGTTTTAGAGCTAGAAATAGCAAGTTA (/sc/arion/projects/BiNGS/bings_omics/engine/software/Mageck) [ulukag01@bings-1 merge_lanes]$ zcat EG03_04_R1_001.fastq.gz |head -n 20 @NB502110:449:HHJH7BGXT:1:11101:24029:1050 1:N:0:TTGAACCG CAACTNTGGAAAGGACGAAACACCGAGCCNNGNATCTCCTTCTGAGTTTTAGAGCTAGAAATAGCAAGTTAAAAT + AAAAA#EA6EEEEEEEE//EE6AEA/E/E##A#EE<<AEE///EA/E/EE</E/<AAA/AEE/<<EEEA/EE/EE @NB502110:449:HHJH7BGXT:1:11101:26316:1053 1:N:0:TTGAACCG ACGCAACTTGTGGAAAGGACGAAACACCGGNCNGCGGCAAAGCGCACTGGTTTTAGAGCTAGAAATAGCAAGTTA + /AAAAEE6EEEEEEEEEEEEEEEEEEEE/E#E#EAEEEEEAEAAEEEEAAEEEEEEEEEEEEEEEEEEEEEAEEA @NB502110:449:HHJH7BGXT:1:11101:16860:1053 1:N:0:TTGGACCG ACGCAACTTGTGGAAAGGACGAAACACCGGNGNGGTCTTTCGACCACTCGTTTTAGAGCTAGAAATAGCAAGTTA + AAAAAEEEEEEEEEEEEEEEEE/EEEEEEE#E#EEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEE @NB502110:449:HHJH7BGXT:1:11101:11183:1054 1:N:0:TTGAACCG TGCACCTTGTGGAAAGGACGAAACACCGCCATNGCAGATGGTGACAGGGTTTTAGAGCTAGAAATAGCAAGTTAA + AA//A/EE///EAE6EEEEEEEEEAEAEEEEE#/EEEEEE6EAEEE//E//EEEEAEE<EEEEE/EEEEEEA<EE @NB502110:449:HHJH7BGXT:1:11101:8760:1055 1:N:0:TTGAACCG TTGTGGAAAGGACGAAACACCGGATGCTTACCNAGTAATCATGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAG + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
daoyingiris
Hello everyone, I am here in search of help to know the tool mageck better a s I am facing problem in allignling my reads on library file. ZerosgRNA is having 0 count. Can you help me in this??