Chad Mansfield

No worries! Thank you for the reply. I appreciate your help. I'll let you know how it works out. On Mon, Feb 28, 2022 at 9:13 PM Mikhail Kolmogorov ***@***.***>...

I used hisat2 to align my raw reads to my.scaffolds to produce my.aligned.bam. scaffold4,190040,f7622z26696k7a0m100_f134738Z163344 is not present in my.aligned.bam. My best guess is I had no transcripts from that region?

head my.bam.samtoolsview.txt @HD VN:1.0 SO:coordinate @SQ SN:scaffold1,184907,f53044Z184907 LN:184907 @SQ SN:scaffold2,183271,f116433Z183271 LN:183271 @SQ SN:scaffold3,168908,f16799Z168908 LN:168908 @SQ SN:scaffold4,190040,f7622z26696k4a0m100_f134738Z163344 LN:190140 @SQ SN:scaffold5,176065,r80173z25589k5a0m100_f144949Z150476 LN:176165 @SQ SN:scaffold6,187668,f107299Z144999k4a0m100_f16915z42669 LN:187768 @SQ SN:scaffold7,141766,f45237Z141766 LN:141766 @SQ SN:scaffold8,189576,f6z51182k16a0m100_f108676Z138394 LN:189676 @SQ...

I used samtools view to convert to a bam file and then used samtools sort to sort my bam file. I tried renaming the scaffolds by numbers (1-x) and had...

hisat2 -x snail -p 10 --very-sensitive -1 M9-S3_R1_001.fastq.gz -2 M9-S3_R2_001.fastq.gz \\ -S ./align/my.aligned.sam --summary-file ./align/summary/M9-S3.txt --new-summary samtools view -b -@ 8 my.aligned.sam | samtools sort -@ 8 > my.aligned.sort.bam

grep "scaffold4,190040,f7622z26696k7a0m100_f134738Z163344" my.scaffolds >scaffold4,190040,f7622z26696k7a0m100_f134738Z163344 It's there.

I really appreciate your help. I'll give that a try and see how it works.

> not sure what `**I had to go with the default species because I kept getting errors when I would change it.` - can you clarify where you had trouble...