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Old 03-28-2018, 06:32 AM   #5
MariaF
Junior Member
 
Location: Russia

Join Date: Mar 2018
Posts: 4
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Thanks for your attention to my problem, GenoMax.

samtools view -H temp.samheader.sam
Quote:
@HD VN:1.0 SO:unsorted
@SQ SN:0_2.65543%_cov_993_len_552 LN:552
@SQ SN:1_2.28932%_cov_1093_len_446 LN:446
samtools view -H test_genome.bwt.samheader.sam
Quote:
@HD VN:1.0 SO:coordinate
@SQ SN:0_2.65543%_cov_993_len_552 LN:552
@SQ SN:10_0.802277%_cov_294_len_562 LN:562
samtools view -H accepted_hits.bam
Quote:
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:249250621
@SQ SN:chr10 LN:135534747
I guess I downloaded the wrong annotation because I see this in the sample-file sample_count.txt:
Quote:
A1BG 226
A1BG-AS1 202
A1CF 5
However, my .gtf file doesn't contain such names of genes. I can't find the annotation hg19 from UCSC which include such names.
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