[?2004h(base) gskoksharova@genedev2:~$ cd /sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams [?2004l [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams$ s amtools [?2004l Program: samtools (Tools for alignments in the SAM format) Version: 1.13 (using htslib 1.13+ds) Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA fqidx index/extract FASTQ index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates ampliconclip clip oligos from the end of reads -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA import Converts FASTA or FASTQ files to SAM/BAM/CRAM -- Statistics bedcov read depth per BED region coverage alignment depth and percent coverage depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) ampliconstats generate amplicon specific stats -- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM -- Misc help [cmd] display this help message or help for [cmd] version detailed version information [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams$ s amtools index *.bam [?2004l [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams$ f or bam oin SGNex_Hct116_cDNA_replicate1_run6.bam SGNex_Hct116_cDNA_replicate3_run3.bam SGNex_Hct116_cDNA_replicate4_run2.bam SGNex_Hct116_directcDNA_replicate1_run4.bam SGNex_Hct116_directcDNA_replicate1_run5.bam SGNex_Hct116_directcDNA_replicate3_run2.bam SGNex_Hct116_directcDNA_replicate4_run1.bam; do samtools index $ {}b}a}m}; done [?2004l [E::hts_hopen] Failed to open file SGNex_Hct116_cDNA_replicate3_run3.bam [E::hts_open_format] Failed to open file "SGNex_Hct116_cDNA_replicate3_run3.bam" : Exec format error samtools index: failed to open "SGNex_Hct116_cDNA_replicate3_run3.bam": Exec format error [E::hts_open_format] Failed to open file "SGNex_Hct116_directcDNA_replicate4_run1.bam" : No such file or directory samtools index: failed to open "SGNex_Hct116_directcDNA_replicate4_run1.bam": No such file or directory [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams$ f ile SGNex_Hct116_cDNA_replicate3_run3.bam [?2004l SGNex_Hct116_cDNA_replicate3_run3.bam: SAMtools BAI (BAM indexing format), with 196 reference sequences [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams$ f ile SGNex_Hct116_cDNA_replicate4_run2.bam [?2004l SGNex_Hct116_cDNA_replicate4_run2.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 2899 [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/SGNex_bams$ c d /sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes [?2004l [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$ M(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$ conda activate tools [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$ samtools index /sf/storage/gmo/hic/out/by_User/Galya/misc/misc_for_sirius/LepOgor4-1/LepOgor-4-1.rescaled.bam [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$ samtools faidx /sf/storage/gmo/hic/out/by_User/Galya/misc/misc_for_sirius/LepOgor4-1/LepusTolai_NC_025748.1.fasta [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$ ыфьещщды афшвчsamtools faidx /sf/storage/gmo/hic/out/by_User/Galya/misc/misc_for_sirius/OSch-3/OvisAries_NC_001941.1.fasta [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$ samtools index /sf/storage/gmo/hic/out/by_User/Galya/misc/misc_for_sirius/OSch-3/ArtemOSch3.rescaled.bam [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/misc/teaching_files/genomes$